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Implementation of a generic docking algorithm (#677)
* Implementation of docking algorithm Signed-off-by: cplett <[email protected]> * Update Docking Algorithm Signed-off-by: cplett <[email protected]> * Update docking algorithm for QCG use Signed-off-by: cplett <[email protected]> Signed-off-by: cplett <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| # This file is part of xtb. | ||
| # | ||
| # Copyright (C) 2022 Sebastian Ehlert, Christoph Plett | ||
| # | ||
| # xtb is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Lesser General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # xtb is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU Lesser General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU Lesser General Public License | ||
| # along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
|
||
| set(dir "${CMAKE_CURRENT_SOURCE_DIR}") | ||
|
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| list(APPEND srcs | ||
| "${dir}/param.f90" | ||
| "${dir}/search_nci.f90" | ||
| "${dir}/set_module.f90" | ||
| ) | ||
|
|
||
| set(srcs ${srcs} PARENT_SCOPE) |
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|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| # This file is part of xtb. | ||
| # | ||
| # Copyright (C) 2022 Sebastian Ehlert, Christoph Plett | ||
| # | ||
| # xtb is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Lesser General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # xtb is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU Lesser General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU Lesser General Public License | ||
| # along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
|
||
| srcs += files( | ||
| 'search_nci.f90', | ||
| 'param.f90', | ||
| 'set_module.f90', | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| # This file is part of xtb. | ||
| # | ||
| # Copyright (C) 2022 Sebastian Ehlert, Christoph Plett | ||
| # | ||
| # xtb is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Lesser General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # xtb is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU Lesser General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU Lesser General Public License | ||
| # along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
|
||
| set(dir "${CMAKE_CURRENT_SOURCE_DIR}") | ||
|
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| list(APPEND srcs | ||
| "${dir}/calculator.f90" | ||
| "${dir}/data.f90" | ||
| "${dir}/iff_energy.f90" | ||
| "${dir}/iff_ini.f90" | ||
| "${dir}/iff_lmo.f90" | ||
| "${dir}/iff_prepare.f90" | ||
| ) | ||
|
|
||
| set(srcs ${srcs} PARENT_SCOPE) |
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|---|---|---|
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| ! This file is part of xtb. | ||
| ! | ||
| ! Copyright (C) 2022 Stefan Grimme | ||
| ! | ||
| ! xtb is free software: you can redistribute it and/or modify it under | ||
| ! the terms of the GNU Lesser General Public License as published by | ||
| ! the Free Software Foundation, either version 3 of the License, or | ||
| ! (at your option) any later version. | ||
| ! | ||
| ! xtb is distributed in the hope that it will be useful, | ||
| ! but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| ! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| ! GNU Lesser General Public License for more details. | ||
| ! | ||
| ! You should have received a copy of the GNU Lesser General Public License | ||
| ! along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
|
||
| !> Intermolecular force field calculator | ||
| module xtb_iff_calculator | ||
| use xtb_mctc_accuracy, only: wp | ||
| use xtb_type_calculator, only: TCalculator | ||
| use xtb_type_environment, only: TEnvironment | ||
| use xtb_type_molecule, only: TMolecule, init | ||
| use xtb_type_restart | ||
| use xtb_iff_data, only: TIFFData | ||
| use xtb_type_data, only: scc_results | ||
| use xtb_iff_iffenergy, only: iff_e | ||
| use xtb_docking_param | ||
| use xtb_iff_iffini, only : init_iff | ||
|
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||
| implicit none | ||
|
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| private | ||
|
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| public :: TIFFCalculator, newIFFCalculator | ||
|
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| !> Calculator interface for xTB based methods | ||
| type, extends(TCalculator) :: TIFFCalculator | ||
|
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| type(TIFFData) :: dat | ||
|
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| contains | ||
|
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| !> Perform xTB single point calculationV | ||
| procedure :: singlepoint | ||
|
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| !> Write informative printout | ||
| procedure :: writeInfo | ||
|
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| end type TIFFCalculator | ||
|
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| character(len=*), private, parameter :: outfmt = & | ||
| '(9x,"::",1x,a,f23.12,1x,a,1x,"::")' | ||
|
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| contains | ||
|
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| subroutine newIFFCalculator(env, comb, iff_data, calc) | ||
|
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| character(len=*), parameter :: source = 'main_setup_newIFFCalculator' | ||
|
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| type(TEnvironment), intent(inout) :: env | ||
|
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| !> Combined structure of molA and molB (molA has to be first) | ||
| type(TMolecule), intent(in) :: comb | ||
|
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| type(TIFFData), intent(in) :: iff_data | ||
|
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| type(TIFFCalculator), intent(out) :: calc | ||
|
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| integer, allocatable :: at(:) | ||
| real(wp), allocatable :: xyz(:,:) | ||
| logical :: exitRun | ||
| real(wp) :: molA_e,molB_e | ||
| character(len=:), allocatable :: fnam | ||
| real(wp) :: icoord(6), icoord0(6) | ||
| real(wp) :: rlmo2(4,(comb%n-natom_molA)*10) | ||
|
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| call set_iff_param | ||
| call calc%dat%allocateIFFData(natom_molA,comb%n-natom_molA) | ||
| calc%dat = iff_data | ||
|
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| xyz=calc%dat%xyz2 | ||
| rlmo2=calc%dat%rlmo2 | ||
|
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| call init_iff(env,calc%dat%n1,calc%dat%n2,calc%dat%at1,calc%dat%at2,& | ||
| & calc%dat%neigh,calc%dat%xyz1,calc%dat%xyz2,calc%dat%q1,& | ||
| & calc%dat%q2,calc%dat%c6ab,calc%dat%z1,calc%dat%z2,& | ||
| & calc%dat%cprob,calc%dat%nlmo1,calc%dat%nlmo2,calc%dat%lmo1,calc%dat%lmo2,& | ||
| & calc%dat%qdr1,calc%dat%qdr2,calc%dat%rlmo1,calc%dat%rlmo2,& | ||
| & calc%dat%cn1,calc%dat%cn2,calc%dat%alp1,calc%dat%alp2,calc%dat%alpab,& | ||
| & calc%dat%den1,calc%dat%den2,calc%dat%gab1,calc%dat%gab2,calc%dat%qcm1,& | ||
| & calc%dat%qcm2,calc%dat%n,calc%dat%at,calc%dat%xyz,calc%dat%q,icoord,icoord0,& | ||
| & .false.) | ||
| calc%dat%xyz2=xyz | ||
| calc%dat%rlmo2=rlmo2 | ||
|
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| call env%check(exitRun) | ||
| if (exitRun) then | ||
| call env%error("Could not create IFF calculator", source) | ||
| return | ||
| end if | ||
|
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||
| end subroutine newIFFCalculator | ||
|
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| subroutine singlepoint(self, env, mol, chk, printlevel, restart, & | ||
| & energy, gradient, sigma, hlgap, results) | ||
|
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| !> Source of the generated errors | ||
| character(len=*), parameter :: source = 'iff_calculator_singlepoint' | ||
|
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| !> Calculator instance | ||
| class(TIFFCalculator), intent(inout) :: self | ||
|
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| !> Computational environment | ||
| type(TEnvironment), intent(inout) :: env | ||
|
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| !> Molecular structure data | ||
| type(TMolecule), intent(inout) :: mol | ||
|
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| !> Wavefunction data | ||
| type(TRestart), intent(inout) :: chk | ||
|
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| !> Print level for IO | ||
| integer, intent(in) :: printlevel | ||
|
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| !> Restart from previous results | ||
| logical, intent(in) :: restart | ||
|
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| !> Total energy | ||
| real(wp), intent(out) :: energy | ||
|
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| !> Molecular gradient | ||
| real(wp), intent(out) :: gradient(:, :) | ||
|
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| !> Strain derivatives | ||
| real(wp), intent(out) :: sigma(:, :) | ||
|
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| !> HOMO-LUMO gab | ||
| real(wp), intent(out) :: hlgap | ||
|
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| !> Detailed results | ||
| type(scc_results), intent(out) :: results | ||
|
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| call iff_e(env, self%dat%n, self%dat%n1, self%dat%n2, self%dat%at1,& | ||
| & self%dat%at2, self%dat%neigh, self%dat%xyz1, self%dat%xyz2,& | ||
| & self%dat%q1, self%dat%q2, self%dat%c6ab, self%dat%z1, self%dat%z2,& | ||
| & self%dat%nlmo1, self%dat%nlmo2, self%dat%lmo1, self%dat%lmo2,& | ||
| & self%dat%rlmo1, self%dat%rlmo2,self%dat%qdr1, self%dat%qdr2,& | ||
| & self%dat%cn1, self%dat%cn2, self%dat%alp1,& | ||
| & self%dat%alp2, self%dat%alpab, self%dat%qct1, self%dat%qct2,& | ||
| & self%dat%den1, self%dat%den2, self%dat%gab1, self%dat%gab2,& | ||
| & .true., 0, energy) | ||
|
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| results%e_total=energy | ||
| gradient = 0 | ||
| sigma = 0 | ||
| hlgap = 0 | ||
|
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| end subroutine singlepoint | ||
|
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||
| subroutine writeInfo(self, unit, mol) | ||
|
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| !> Calculator instance | ||
| class(TIFFCalculator), intent(in) :: self | ||
|
|
||
| !> Unit for I/O | ||
| integer, intent(in) :: unit | ||
|
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| !> Molecular structure data | ||
| type(TMolecule), intent(in) :: mol | ||
|
|
||
| end subroutine writeInfo | ||
|
|
||
| end module xtb_iff_calculator |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,191 @@ | ||
| ! This file is part of xtb. | ||
| ! | ||
| ! Copyright (C) 2022 Christoph Plett | ||
| ! | ||
| ! xtb is free software: you can redistribute it and/or modify it under | ||
| ! the terms of the GNU Lesser General Public License as published by | ||
| ! the Free Software Foundation, either version 3 of the License, or | ||
| ! (at your option) any later version. | ||
| ! | ||
| ! xtb is distributed in the hope that it will be useful, | ||
| ! but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| ! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| ! GNU Lesser General Public License for more details. | ||
| ! | ||
| ! You should have received a copy of the GNU Lesser General Public License | ||
| ! along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
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||
| !> Topological data for force field type calculations | ||
| module xtb_iff_data | ||
| use xtb_mctc_accuracy, only: wp | ||
| use xtb_type_molecule, only: TMolecule | ||
| implicit none | ||
| private | ||
|
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| public :: TIFFData | ||
|
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| type :: TIFFData | ||
|
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| !> Total number of atoms | ||
| integer :: n | ||
|
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| !> Number of atoms molA and B | ||
| integer :: n1 | ||
| integer :: n2 | ||
|
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| !> Number of LMOs molA and B | ||
| integer :: nlmo1 | ||
| integer :: nlmo2 | ||
|
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| !> Coordinates molA and B and whole system | ||
| real(wp), allocatable :: xyz1(:, :) | ||
| real(wp), allocatable :: xyz2(:, :) | ||
| real(wp), allocatable :: xyz(:, :) | ||
|
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| !> LMO positions molA and B | ||
| real(wp), allocatable :: rlmo1(:, :) | ||
| real(wp), allocatable :: rlmo2(:, :) | ||
|
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| !> Charges | ||
| real(wp), allocatable :: q1(:) | ||
| real(wp), allocatable :: q2(:) | ||
| real(wp), allocatable :: q(:) | ||
|
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| !> Deviation from atomic charge | ||
| real(wp), allocatable :: qdr1(:) | ||
| real(wp), allocatable :: qdr2(:) | ||
|
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| !> Deviation from atomic position | ||
| real(wp), allocatable ::xyzdr1(:, :) | ||
| real(wp), allocatable ::xyzdr2(:, :) | ||
|
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| !> Coordination numbers | ||
| real(wp), allocatable :: cn1(:) | ||
| real(wp), allocatable :: cn2(:) | ||
| real(wp), allocatable :: cn(:) | ||
|
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||
| !> Electron count per element | ||
| real(wp), allocatable :: z1(:) | ||
| real(wp), allocatable :: z2(:) | ||
|
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| !> Polarizabilities | ||
| real(wp), allocatable :: alp1(:) | ||
| real(wp), allocatable :: alp2(:) | ||
| real(wp), allocatable :: alpab(:, :) | ||
| real(wp), allocatable :: alp0(:) | ||
|
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||
| !> Ordinary number | ||
| integer, allocatable :: at1(:) | ||
| integer, allocatable :: at2(:) | ||
| integer, allocatable :: at(:) | ||
|
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||
| !> LMO values | ||
| integer, allocatable :: lmo1(:) | ||
| integer, allocatable :: lmo2(:) | ||
|
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||
| !> C6 coeffs for the whole system | ||
| real(wp), allocatable :: c6ab(:, :) | ||
|
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||
| !> C6 coeffs for molA with rare gas | ||
| real(wp), allocatable :: cprob(:) | ||
|
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||
| real(wp), allocatable :: gab1(:, :) | ||
| real(wp), allocatable :: gab2(:, :) | ||
|
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| !> Frontier orbital densities | ||
| real(wp), allocatable :: den1(:, :, :) | ||
| real(wp), allocatable :: den2(:, :, :) | ||
|
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||
| !> Charge related stuff (from GFN2 calc.) | ||
| real(wp), allocatable :: qcm1(:) | ||
| real(wp), allocatable :: qcm2(:) | ||
| real(wp), allocatable :: qct1(:, :) | ||
| real(wp), allocatable :: qct2(:, :) | ||
|
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||
| !> Neighbour list | ||
| integer, allocatable :: neigh(:, :) | ||
|
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| contains | ||
|
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| procedure :: delete | ||
| procedure :: allocateIFFData | ||
|
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| end type TIFFData | ||
|
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| contains | ||
|
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| subroutine delete(self) | ||
| class(TIFFData), intent(out) :: self | ||
|
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||
| if (allocated(self%xyz1)) deallocate (self%xyz1) | ||
| if (allocated(self%rlmo1)) deallocate (self%rlmo1) | ||
| if (allocated(self%q1)) deallocate (self%q1) | ||
| if (allocated(self%qdr1)) deallocate (self%qdr1) | ||
| if (allocated(self%xyzdr1)) deallocate (self%xyzdr1) | ||
| if (allocated(self%cn1)) deallocate (self%cn1) | ||
| if (allocated(self%z1)) deallocate (self%z1) | ||
| if (allocated(self%alp1)) deallocate (self%alp1) | ||
| if (allocated(self%qct1)) deallocate (self%qct1) | ||
| if (allocated(self%at1)) deallocate (self%at1) | ||
| if (allocated(self%lmo1)) deallocate (self%lmo1) | ||
| if (allocated(self%xyz2)) deallocate (self%xyz2) | ||
| if (allocated(self%rlmo2)) deallocate (self%rlmo2) | ||
| if (allocated(self%q2)) deallocate (self%q2) | ||
| if (allocated(self%qdr2)) deallocate (self%qdr2) | ||
| if (allocated(self%xyzdr2)) deallocate (self%xyzdr2) | ||
| if (allocated(self%cn2)) deallocate (self%cn2) | ||
| if (allocated(self%z2)) deallocate (self%z2) | ||
| if (allocated(self%alp2)) deallocate (self%alp2) | ||
| if (allocated(self%qct2)) deallocate (self%qct2) | ||
| if (allocated(self%at2)) deallocate (self%at2) | ||
| if (allocated(self%lmo2)) deallocate (self%lmo2) | ||
| if (allocated(self%c6ab)) deallocate (self%c6ab) | ||
| if (allocated(self%alpab)) deallocate (self%alpab) | ||
| if (allocated(self%cprob)) deallocate (self%cprob) | ||
| if (allocated(self%xyz)) deallocate (self%xyz) | ||
| if (allocated(self%q)) deallocate (self%q) | ||
| if (allocated(self%cn)) deallocate (self%cn) | ||
| if (allocated(self%alp0)) deallocate (self%alp0) | ||
| if (allocated(self%gab1)) deallocate (self%gab1) | ||
| if (allocated(self%gab2)) deallocate (self%gab2) | ||
| if (allocated(self%den1)) deallocate (self%den1) | ||
| if (allocated(self%den2)) deallocate (self%den2) | ||
| if (allocated(self%qcm1)) deallocate (self%qcm1) | ||
| if (allocated(self%qcm2)) deallocate (self%qcm2) | ||
| if (allocated(self%at)) deallocate (self%at) | ||
| if (allocated(self%neigh)) deallocate (self%neigh) | ||
|
|
||
| end subroutine delete | ||
|
|
||
| subroutine allocateIFFData(self, n1, n2) | ||
|
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| class(TIFFData), intent(out) :: self | ||
|
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||
| integer, intent(in) :: n1, n2 | ||
|
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| integer :: n | ||
|
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||
| self%n1 = n1 | ||
| self%n2 = n2 | ||
|
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||
| !Allocate Infos of molA | ||
| allocate(self%at1(n1),self%xyz1(3,n1),self%rlmo1(4,10*n1),self%q1(n1),self%lmo1(10*n1),& | ||
| &self%cn1(n1),self%alp1(n1),self%qct1(n1,2),self%qdr1(n1),self%xyzdr1(3,n1),& | ||
| &self%z1(n1), self%den1(2, 4, n1), self%gab1(n1, n1), self%qcm1(n1)) | ||
| self%rlmo1 = 0.0_wp | ||
|
|
||
| !Allocate Infos of molB | ||
| allocate(self%at2(n2),self%xyz2(3,n2),self%rlmo2(4,10*n2),self%q2(n2),self%lmo2(10*n2),& | ||
| & self%cn2(n2),self%alp2(n2),self%qct2(n2,2),self%qdr2(n2),self%xyzdr2(3,n2),& | ||
| & self%z2(n2), self%den2(2, 4, n2), self%gab2(n2, n2), self%qcm2(n2)) | ||
| self%rlmo2 = 0.0_wp | ||
|
|
||
| !Allocate combined Infos | ||
| self%n = n1 + n2 | ||
| n = self%n | ||
| allocate(self%at(n),self%xyz(3,n),self%q(n),self%c6ab(n,n),self%alp0(n),self%cn(n),self%neigh(0:n,n),& | ||
| & self%alpab(n2, n1), self%cprob(n1)) | ||
|
|
||
| end subroutine allocateIFFData | ||
|
|
||
| end module xtb_iff_data |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,241 @@ | ||
| ! This file is part of xtb. | ||
| ! | ||
| ! Copyright (C) 2022 Christoph Plett | ||
| ! | ||
| ! xtb is free software: you can redistribute it and/or modify it under | ||
| ! the terms of the GNU Lesser General Public License as published by | ||
| ! the Free Software Foundation, either version 3 of the License, or | ||
| ! (at your option) any later version. | ||
| ! | ||
| ! xtb is distributed in the hope that it will be useful, | ||
| ! but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| ! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| ! GNU Lesser General Public License for more details. | ||
| ! | ||
| ! You should have received a copy of the GNU Lesser General Public License | ||
| ! along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
|
||
| module xtb_iff_iffprepare | ||
| use xtb_mctc_accuracy, only: wp | ||
| use xtb_type_environment, only: TEnvironment | ||
| use xtb_splitparam | ||
| use xtb_iff_calculator, only: TIFFCalculator | ||
| use xtb_iff_data, only: TIFFData | ||
| use xtb_type_atomlist | ||
| use xtb_type_molecule, only: TMolecule | ||
| use xtb_setparam | ||
| use xtb_type_restart, only: TRestart | ||
| use xtb_type_calculator, only: TCalculator | ||
| use xtb_xtb_calculator, only: TxTBCalculator | ||
| use xtb_setmod, only: set_gfn | ||
| use xtb_readin, only: xfind | ||
| use xtb_solv_state, only: solutionState | ||
| use xtb_type_data, only: scc_results | ||
| use xtb_main_defaults, only: initDefaults | ||
| use xtb_disp_ncoord, only: ncoord_gfn, ncoord_erf | ||
| use xtb_scc_core, only: iniqshell | ||
| use xtb_eeq, only: goedecker_chrgeq | ||
| use xtb_main_setup, only: newCalculator | ||
| use xtb_single, only: singlepoint | ||
| use xtb_docking_param, only: chrg, uhf, gsolvstate_iff, pre_e_A, & | ||
| & pre_e_B, optlvl, ehomo, elumo, dipol, & | ||
| & natom_molA, natom_arg, split_mol | ||
|
|
||
| implicit none | ||
|
|
||
| private | ||
| public :: prepare_IFF, precomp | ||
|
|
||
| contains | ||
|
|
||
| subroutine prepare_IFF(env, comb, iff_data) | ||
|
|
||
| type(TEnvironment), intent(inout) :: env | ||
| !> Combined structure of molA and molB (molA has to be first) | ||
| type(TMolecule), intent(in) :: comb | ||
| !> IFF data | ||
| type(TIFFData) :: iff_data | ||
|
|
||
| character(len=*), parameter :: source = 'preperation_IFFCalculator' | ||
| type(TMolecule) :: molA, molB | ||
| integer, allocatable :: at(:) | ||
| real(wp), allocatable :: xyz(:, :) | ||
| real(wp) :: molA_e, molB_e | ||
| integer, allocatable :: list(:) | ||
| type(TAtomList) :: atl | ||
|
|
||
| call atl%resize(comb%n) | ||
|
|
||
| !> First make the argument natom_arg to a list of number of atoms | ||
| call atl%new(natom_arg) | ||
| if (atl%get_error()) then | ||
| call env%warning('something is wrong in the fixing list',source) | ||
| return | ||
| endif | ||
| call atl%to_list(list) | ||
|
|
||
| molA%n = size(list) | ||
| natom_molA = molA%n | ||
| molB%n = comb%n - molA%n | ||
|
|
||
| if (natom_molA == 0) call env%error('No atoms of Molecule A given') | ||
| if(natom_molA > comb%n) & | ||
| & call env%error('More atoms of Molecule A than contained in structure') | ||
|
|
||
| call split_mol(molA, molB, size(list), list, comb) | ||
| call iff_data%allocateIFFData(molA%n, molB%n) | ||
|
|
||
| call precomp(env, iff_data, molA, molA_e, 1) | ||
| call precomp(env, iff_data, molB, molB_e, 2) | ||
|
|
||
| end subroutine prepare_IFF | ||
|
|
||
| subroutine precomp(env, iff_data, mol, etot, mol_num) | ||
|
|
||
| !> Molecular structure data | ||
| type(TMolecule), intent(inout) :: mol | ||
| !> IFF data | ||
| type(TIFFData), intent(inout) :: iff_data | ||
| !> Calculation environment | ||
| type(TEnvironment), intent(inout) :: env | ||
| integer, intent(in) :: mol_num | ||
|
|
||
| class(TCalculator), allocatable :: calc | ||
| type(TRestart) :: chk | ||
| character(len=:), allocatable :: fnv !parameter file | ||
| logical :: restart = .false. | ||
| real(wp) :: acc = 1.0_wp !SCF accuracy | ||
| real(wp) :: egap | ||
| integer :: gsolvstate !Should be gas | ||
| real(wp), allocatable :: cn(:) | ||
| real(wp), allocatable :: dcn(:, :, :), dq(:, :, :), g(:, :) | ||
| real(wp) :: er | ||
| integer, external :: ncore | ||
| logical :: lgrad | ||
| logical :: exist | ||
| real(wp), intent(out) :: etot | ||
| real(wp) :: sigma(3, 3) | ||
| type(scc_results) :: res | ||
| integer :: i | ||
| integer :: extrun_tmp | ||
| integer, allocatable :: tmp_unit | ||
| logical :: newdisp_tmp | ||
| integer :: itemp = 48 | ||
|
|
||
| allocate (cn(mol%n), g(3, mol%n)) | ||
|
|
||
| set%pr_lmo = .true. | ||
| set%silent = .true. | ||
|
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||
| !Setting up z | ||
| do i = 1, mol%n | ||
| mol%z(i) = mol%at(i) - ncore(mol%at(i)) | ||
| ! lanthanides without f are treated as La | ||
| if (mol%at(i) .gt. 57 .and. mol%at(i) .lt. 72) mol%z(i) = 3 | ||
| end do | ||
|
|
||
| !> Set GFN2 settings | ||
| if (optlvl /= 'gfn1') then | ||
| set%gfn_method = 2 | ||
| fnv = xfind('param_gfn2-xtb.txt') | ||
| extrun_tmp = set%mode_extrun | ||
| set%mode_extrun = p_ext_xtb | ||
| newdisp_tmp = set%newdisp | ||
| set%newdisp = .true. | ||
| else | ||
| fnv = xfind('param_gfn1-xtb.txt') !Other stuff already set | ||
| end if | ||
| if (mol_num .eq. 1) then | ||
| if (chrg(1) /= 0.0_wp) mol%chrg = chrg(1) | ||
| if (uhf(1) /= 0.0_wp) mol%uhf = uhf(1) | ||
| elseif (mol_num .eq. 2) then | ||
| if (chrg(2) /= 0.0_wp) mol%chrg = chrg(2) | ||
| if (uhf(2) /= 0.0_wp) mol%uhf = uhf(2) | ||
| end if | ||
|
|
||
| call open_file(itemp, 'tmp_lmo', 'w') | ||
| tmp_unit = env%unit | ||
| env%unit = itemp | ||
|
|
||
| !> New calculator | ||
| call newCalculator(env, mol, calc, fnv, restart, acc) | ||
| call env%checkpoint("Could not setup parameterisation") | ||
|
|
||
| ! gsolvstate = solutionState%gsolv | ||
| call initDefaults(env, calc, mol, gsolvstate_iff) | ||
| !> initial guess, setup wavefunction | ||
| select type (calc) | ||
| type is (TxTBCalculator) | ||
| calc%etemp = set%etemp | ||
| calc%maxiter = set%maxscciter | ||
| call chk%wfn%allocate(mol%n, calc%basis%nshell, calc%basis%nao) | ||
| !> EN charges and CN | ||
| call ncoord_gfn(mol%n, mol%at, mol%xyz, cn) | ||
| if (mol%npbc > 0) then | ||
| chk%wfn%q = real(set%ichrg, wp)/real(mol%n, wp) | ||
| else | ||
| call ncoord_erf(mol%n, mol%at, mol%xyz, cn) | ||
| call goedecker_chrgeq(mol%n,mol%at,mol%xyz,real(set%ichrg,wp),cn,dcn,chk%wfn%q,dq,er,g,& | ||
| .false., .false., .false.) | ||
| chk%wfn%q = real(set%ichrg, wp)/real(mol%n, wp) | ||
| end if | ||
| !> initialize shell charges from gasteiger charges | ||
| call iniqshell(calc%xtbData,mol%n,mol%at,mol%z,calc%basis%nshell,chk%wfn%q,chk%wfn%qsh,set%gfn_method) | ||
| end select | ||
|
|
||
| call delete_file('.sccnotconverged') | ||
| call delete_file('charges') | ||
|
|
||
| call env%checkpoint("Setup for calculation failed") | ||
|
|
||
| allocate(res%iff_results) | ||
|
|
||
| !> the SP | ||
| call singlepoint & | ||
| & (env, mol, chk, calc, egap, set%etemp, set%maxscciter, 2,& | ||
| & exist, lgrad, acc, etot, g, sigma, res) | ||
|
|
||
| set%pr_lmo = .false. | ||
|
|
||
| !> Save the results | ||
| if (mol_num .eq. 1) then | ||
| pre_e_A = etot | ||
| iff_data%n1 = res%iff_results%n | ||
| iff_data%at1 = res%iff_results%at | ||
| iff_data%xyz1 = res%iff_results%xyz | ||
| iff_data%q1 = res%iff_results%q | ||
| iff_data%nlmo1 = res%iff_results%nlmo | ||
| iff_data%rlmo1 = res%iff_results%rlmo | ||
| iff_data%lmo1 = res%iff_results%lmo | ||
| iff_data%qct1 = res%iff_results%qct | ||
| ehomo(1) = res%iff_results%ehomo | ||
| elumo(1) = res%iff_results%elumo | ||
| dipol(1) = res%iff_results%dipol | ||
| elseif (mol_num .eq. 2) then | ||
| pre_e_B = etot | ||
| iff_data%n2 = res%iff_results%n | ||
| iff_data%at2 = res%iff_results%at | ||
| iff_data%xyz2 = res%iff_results%xyz | ||
| iff_data%q2 = res%iff_results%q | ||
| iff_data%nlmo2 = res%iff_results%nlmo | ||
| iff_data%rlmo2 = res%iff_results%rlmo | ||
| iff_data%lmo2 = res%iff_results%lmo | ||
| iff_data%qct2 = res%iff_results%qct | ||
| ehomo(2) = res%iff_results%ehomo | ||
| elumo(2) = res%iff_results%elumo | ||
| dipol(2) = res%iff_results%dipol | ||
| end if | ||
|
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||
| if (optlvl /= 'gfn1') then | ||
| set%mode_extrun = extrun_tmp | ||
| set%newdisp = newdisp_tmp | ||
| end if | ||
|
|
||
| set%silent = .false. | ||
| env%unit = tmp_unit | ||
| call remove_file(itemp) | ||
| deallocate (cn, g) | ||
|
|
||
| end subroutine precomp | ||
|
|
||
| end module xtb_iff_iffprepare |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| # This file is part of xtb. | ||
| # | ||
| # Copyright (C) 2022 Sebastian Ehlert, Christoph Plett | ||
| # | ||
| # xtb is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Lesser General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # xtb is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU Lesser General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU Lesser General Public License | ||
| # along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
|
||
| srcs += files( | ||
| 'calculator.f90', | ||
| 'data.f90', | ||
| 'iff_energy.f90', | ||
| 'iff_ini.f90', | ||
| 'iff_lmo.f90', | ||
| 'iff_prepare.f90', | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -17,6 +17,7 @@ | |
|
|
||
| prog += files( | ||
| 'argparser.f90', | ||
| 'dock.f90', | ||
| 'info.f90', | ||
| 'main.F90', | ||
| 'primary.f90', | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,176 @@ | ||
| ! This file is part of xtb. | ||
| ! SPDX-Identifier: LGPL-3.0-or-later | ||
| ! | ||
| ! xtb is free software: you can redistribute it and/or modify it under | ||
| ! the terms of the GNU Lesser General Public License as published by | ||
| ! the Free Software Foundation, either version 3 of the License, or | ||
| ! (at your option) any later version. | ||
| ! | ||
| ! xtb is distributed in the hope that it will be useful, | ||
| ! but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| ! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| ! GNU Lesser General Public License for more details. | ||
| ! | ||
| ! You should have received a copy of the GNU Lesser General Public License | ||
| ! along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
|
||
| module test_docking | ||
| use testdrive, only : new_unittest, unittest_type, error_type, check_ => check, test_failed | ||
| implicit none | ||
| private | ||
|
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| public :: collect_docking | ||
|
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| contains | ||
|
|
||
| !> Collect all exported unit tests | ||
| subroutine collect_docking(testsuite) | ||
| !> Collection of tests | ||
| type(unittest_type), allocatable, intent(out) :: testsuite(:) | ||
|
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| testsuite = [ & | ||
| new_unittest("eth_wat", test_dock_eth_wat)]!, & | ||
| ! new_unittest("ellips", test_iff_ellips), & | ||
| ! ] | ||
|
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||
| end subroutine collect_docking | ||
|
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||
|
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||
| subroutine test_dock_eth_wat(error) | ||
| use xtb_type_environment, only: TEnvironment, init | ||
| use xtb_mctc_accuracy, only: wp | ||
| use xtb_type_environment, only: TEnvironment | ||
| use xtb_type_molecule | ||
| use xtb_setparam, only: initrand | ||
| use xtb_mctc_systools | ||
| use xtb_setmod | ||
| use xtb_docking_set_module | ||
| use xtb_docking_param | ||
| use xtb_iff_iffini, only: init_iff | ||
| use xtb_iff_iffprepare, only: precomp | ||
| use xtb_iff_iffenergy | ||
| use xtb_docking_search_nci, only: docking_search | ||
| use xtb_mctc_systools | ||
| use xtb_iff_data, only: TIFFData | ||
| type(error_type), allocatable, intent(out) :: error | ||
| !> All important variables stored here | ||
| type(TIFFData) :: iff_data | ||
| real(wp),parameter :: thr = 1.0e-6_wp | ||
| real(wp) :: icoord0(6),icoord(6) | ||
| integer :: n1 | ||
| integer :: at1(9) | ||
| real(wp) :: xyz1(3,9) | ||
| integer :: n2 | ||
| integer :: at2(3) | ||
| real(wp) :: xyz2(3,3) | ||
| integer,parameter :: n = 12 | ||
| integer :: at(n) | ||
| real(wp) :: xyz(3,n) | ||
| real(wp) :: molA_e, molB_e | ||
|
|
||
| logical, parameter :: restart = .false. | ||
|
|
||
| type(TMolecule) :: molA,molB,comb | ||
| real(wp) :: r(3),e | ||
| integer :: i, j, k | ||
| type(TEnvironment) :: env | ||
| character(len=:), allocatable :: fnam | ||
|
|
||
| logical :: exist | ||
|
|
||
| n1 = 9 | ||
| at1 = [6,6,1,1,1,1,8,1,1] | ||
| xyz1 = reshape(& | ||
| &[-10.23731657240310_wp, 4.49526140160057_wp,-0.01444418438295_wp, & | ||
| & -8.92346521409264_wp, 1.93070071439448_wp,-0.06395255870166_wp, & | ||
| & -11.68223026601517_wp, 4.59275319594179_wp,-1.47773402464476_wp, & | ||
| & -8.87186386250594_wp, 5.99323351202269_wp,-0.34218865473603_wp, & | ||
| & -11.13173905821587_wp, 4.79659470137971_wp, 1.81087156124027_wp, & | ||
| & -8.00237319881732_wp, 1.64827398274591_wp,-1.90766384850460_wp, & | ||
| & -10.57950417459641_wp,-0.08678859323640_wp, 0.45375344239209_wp, & | ||
| & -7.47634978432660_wp, 1.83563324786661_wp, 1.40507877109963_wp, & | ||
| & -11.96440476139715_wp,-0.02296384600667_wp,-0.72783557254661_wp],& | ||
| & shape(xyz1)) | ||
|
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| n2 = 3 | ||
| at2 = [8,1,1] | ||
| xyz2 = reshape(& | ||
| &[-14.55824225787638_wp, 0.85763330814882_wp, 0.00000000000000_wp, & | ||
| & -12.72520790897730_wp, 0.85763330814882_wp, 0.00000000000000_wp, & | ||
| & -15.16924740842229_wp,-0.86379381534203_wp,-0.15285994688912_wp],& | ||
| & shape(xyz2)) | ||
|
|
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| call init(env) | ||
| call init(molA, at1, xyz1) | ||
| call init(molB, at2, xyz2) | ||
| call iff_data%allocateIFFData(molA%n, molB%n) | ||
|
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| call initrand | ||
|
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| call set_iff_param | ||
| fnam = 'xtblmoinfo' | ||
| set%pr_local = .false. | ||
|
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| call precomp(env, iff_data, molA, molA_e, 1) | ||
| call check_(error, molA_e,-11.3943358674_wp, thr=thr) | ||
| call precomp(env, iff_data, molB, molB_e, 2) | ||
|
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| call env%checkpoint("LMO computation failed") | ||
|
|
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| call cmadock(molA%n, molA%n, molA%at, molA%xyz, r) | ||
| do i = 1, 3 | ||
| molA%xyz(i, 1:molA%n) = molA%xyz(i, 1:molA%n) - r(i) | ||
| end do | ||
| call cmadock(molB%n, molB%n, molB%at, molB%xyz, r) | ||
| do i = 1, 3 | ||
| molB%xyz(i, 1:molB%n) = molB%xyz(i, 1:molB%n) - r(i) | ||
| end do | ||
|
|
||
| call init_iff(env, iff_data%n1, iff_data%n2, iff_data%at1, iff_data%at2,& | ||
| & iff_data%neigh, iff_data%xyz1, iff_data%xyz2, iff_data%q1, & | ||
| & iff_data%q2, iff_data%c6ab, iff_data%z1, iff_data%z2,& | ||
| & iff_data%cprob, iff_data%nlmo1, iff_data%nlmo2, iff_data%lmo1, iff_data%lmo2,& | ||
| & iff_data%qdr1, iff_data%qdr2, iff_data%rlmo1, iff_data%rlmo2,& | ||
| & iff_data%cn1, iff_data%cn2, iff_data%alp1, iff_data%alp2, iff_data%alpab,& | ||
| & iff_data%den1, iff_data%den2, iff_data%gab1, iff_data%gab2, iff_data%qcm1,& | ||
| & iff_data%qcm2, iff_data%n, iff_data%at, iff_data%xyz, iff_data%q, icoord, icoord0,& | ||
| & .false.) | ||
|
|
||
| call check_(error, icoord(1) ,-4.5265_wp, thr=1.0e-3_wp) | ||
|
|
||
| call env%checkpoint("Initializing xtb-IFF failed.") | ||
|
|
||
| call iff_e(env, iff_data%n, iff_data%n1, iff_data%n2, iff_data%at1, iff_data%at2,& | ||
| & iff_data%neigh, iff_data%xyz1, iff_data%xyz2, iff_data%q1, iff_data%q2,& | ||
| & iff_data%c6ab, iff_data%z1, iff_data%z2,& | ||
| & iff_data%nlmo1, iff_data%nlmo2, iff_data%lmo1, iff_data%lmo2, & | ||
| & iff_data%rlmo1, iff_data%rlmo2,& | ||
| & iff_data%qdr1, iff_data%qdr2, iff_data%cn1, iff_data%cn2, iff_data%alp1, & | ||
| & iff_data%alp2, iff_data%alpab, iff_data%qct1, iff_data%qct2, & | ||
| & iff_data%den1, iff_data%den2, iff_data%gab1, iff_data%gab2, & | ||
| & set%verbose, 0, e, icoord) | ||
|
|
||
| call check_(error, e,0.07745330953243718_wp, thr=thr) | ||
|
|
||
| call env%checkpoint("xtb-IFF sp computation failed") | ||
|
|
||
| call set_optlvl(env) !Sets the optimization level for search in global parameters | ||
| ! call docking_search(env, molA, molB, n, n1, n2, at1, at2, neigh, xyz1,& | ||
| ! & xyz2, q1, q2, c6ab, z1, z2,& | ||
| ! &nlmo1, nlmo2, lmo1, lmo2, rlmo1, rlmo2,& | ||
| ! &qdr1, qdr2, cn1, cn2, alp1, alp2, alpab, qct1, qct2,& | ||
| ! &den1, den2, gab1, gab2, molA_e, molB_e,& | ||
| ! &cprob, e, icoord, comb) | ||
|
|
||
| ! call env%checkpoint("Docking algorithm failed") | ||
|
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| ! call check_(error, calc%topo%nbond,6) | ||
| ! | ||
| ! call check_(error, res_gff%e_total,-0.76480130317838_wp, thr=thr) | ||
|
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| call molA%deallocate | ||
| call molB%deallocate | ||
|
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||
| end subroutine test_dock_eth_wat | ||
|
|
||
| end module test_docking |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| ! This file is part of xtb. | ||
| ! SPDX-Identifier: LGPL-3.0-or-later | ||
| ! | ||
| ! xtb is free software: you can redistribute it and/or modify it under | ||
| ! the terms of the GNU Lesser General Public License as published by | ||
| ! the Free Software Foundation, either version 3 of the License, or | ||
| ! (at your option) any later version. | ||
| ! | ||
| ! xtb is distributed in the hope that it will be useful, | ||
| ! but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| ! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| ! GNU Lesser General Public License for more details. | ||
| ! | ||
| ! You should have received a copy of the GNU Lesser General Public License | ||
| ! along with xtb. If not, see <https://www.gnu.org/licenses/>. | ||
|
|
||
| module test_iff | ||
| use testdrive, only : new_unittest, unittest_type, error_type, check_ => check, test_failed | ||
| implicit none | ||
| private | ||
|
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| public :: collect_iff | ||
|
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| contains | ||
|
|
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| !> Collect all exported unit tests | ||
| subroutine collect_iff(testsuite) | ||
| !> Collection of tests | ||
| type(unittest_type), allocatable, intent(out) :: testsuite(:) | ||
|
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| testsuite = [ & | ||
| new_unittest("iff_sp", test_iff_sp) & | ||
| ] | ||
|
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| end subroutine collect_iff | ||
|
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||
|
|
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| subroutine test_iff_sp(error) | ||
| use xtb_mctc_accuracy, only : wp | ||
| use xtb_mctc_systools | ||
| use xtb_type_environment | ||
| use xtb_type_options | ||
| use xtb_type_molecule | ||
| use xtb_type_data | ||
| use xtb_setparam | ||
| use xtb_setmod | ||
| use xtb_docking_param | ||
| use xtb_type_restart, only: TRestart | ||
| use xtb_iff_calculator, only : TIFFCalculator, newIFFCalculator | ||
| use xtb_iff_data, only : TIFFData | ||
| use xtb_iff_iffprepare, only : prepare_IFF | ||
| type(error_type), allocatable, intent(out) :: error | ||
| real(wp),parameter :: thr = 1.0e-10_wp | ||
| integer, parameter :: nat = 6 | ||
| integer, parameter :: at(nat) = [8,1,1,8,1,1] | ||
| real(wp),parameter :: xyz(3,nat) = reshape(& | ||
| &[-0.04394313126682_wp,-0.15162589575685_wp,-0.12104386666899_wp, & | ||
| & 1.57021196791551_wp, 0.39852223676357_wp,-0.74238980424452_wp, & | ||
| & -0.52096572705612_wp,-1.61453119575215_wp,-1.08142949421996_wp, & | ||
| & -3.35527313086215_wp, 3.63311912367937_wp,-1.97688072772302_wp, & | ||
| & -4.33218397586988_wp, 4.42399249914350_wp,-0.67195282333972_wp, & | ||
| & -2.30284007732108_wp, 2.38679302539156_wp,-1.14422985849389_wp],& | ||
| & shape(xyz)) | ||
|
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| type(TMolecule) :: mol | ||
| type(TEnvironment) :: env | ||
| type(TIFFCalculator) :: calc | ||
| type(TIFFData) :: iff_data | ||
|
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| real(wp) :: etot,egap | ||
| real(wp), allocatable :: g(:,:) | ||
| type(TRestart) :: chk | ||
| real(wp) :: sigma(3,3) | ||
| type(scc_results) :: res | ||
|
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||
|
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| logical :: exist | ||
|
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| call init(env) | ||
| call init(mol,at,xyz) | ||
|
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| natom_arg = '1-3' | ||
| call prepare_IFF(env, mol, iff_data) | ||
| call env%checkpoint("Could not generate electronic properties for IFF") | ||
|
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| call newIFFCalculator(env, mol, iff_data, calc) | ||
|
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| call env%checkpoint("xtb-IFF parameter setup failed") | ||
|
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| allocate( g(3,mol%n), source = 0.0_wp ) | ||
|
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| call calc%singlepoint(env, mol, chk, 2, exist, etot, g, sigma, egap, res) | ||
| write(*,*) 'WW', etot | ||
|
|
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| call check_(error, etot,-0.002628051951328639_wp, thr=thr) | ||
|
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| call mol%deallocate | ||
|
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| end subroutine test_iff_sp | ||
|
|
||
| end module test_iff |