From 816e70a683ea6550c33d1d942080b79b82009fcf Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 14 Dec 2017 19:03:51 +0100 Subject: [PATCH 1/2] Added symmetry detection --- plugins/Symmetry/NEEDED_CHILDREN_MODULES | 1 + plugins/Symmetry/README.rst | 12 + plugins/Symmetry/Symmetry.main.irp.f | 30 +++ plugins/Symmetry/aos.irp.f | 113 ++++++++ plugins/Symmetry/find_sym.irp.f | 318 +++++++++++++++++++++++ src/Nuclei/inertia.irp.f | 32 +++ src/Nuclei/nuclei.irp.f | 149 ++++++++++- 7 files changed, 652 insertions(+), 3 deletions(-) create mode 100644 plugins/Symmetry/NEEDED_CHILDREN_MODULES create mode 100644 plugins/Symmetry/README.rst create mode 100644 plugins/Symmetry/Symmetry.main.irp.f create mode 100644 plugins/Symmetry/aos.irp.f create mode 100644 plugins/Symmetry/find_sym.irp.f create mode 100644 src/Nuclei/inertia.irp.f diff --git a/plugins/Symmetry/NEEDED_CHILDREN_MODULES b/plugins/Symmetry/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..7ea84ba4 --- /dev/null +++ b/plugins/Symmetry/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Bitmask Nuclei Determinants diff --git a/plugins/Symmetry/README.rst b/plugins/Symmetry/README.rst new file mode 100644 index 00000000..ba643f88 --- /dev/null +++ b/plugins/Symmetry/README.rst @@ -0,0 +1,12 @@ +======== +Symmetry +======== + +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. diff --git a/plugins/Symmetry/Symmetry.main.irp.f b/plugins/Symmetry/Symmetry.main.irp.f new file mode 100644 index 00000000..d8d2f350 --- /dev/null +++ b/plugins/Symmetry/Symmetry.main.irp.f @@ -0,0 +1,30 @@ +program Symmetry + implicit none + BEGIN_DOC +! TODO + END_DOC + integer :: n_sym_points, i, j + double precision, allocatable :: tmp(:,:), sym_points(:,:) + character*8 :: sym + n_sym_points = 3 + + print *, 'Molecule is linear:', molecule_is_linear + print *, 'Has center of inversion:', molecule_has_center_of_inversion + print *, 'Symmetry rotation axis:', sym_rotation_axis(:) + call find_symmetry(sym) + print *, 'Group:'//sym + return + allocate(tmp(n_sym_points,n_det), sym_points(3,n_sym_points)) + + call generate_sym_coord(n_sym_points,sym_points) + call compute_sym_det_values(sym_points,n_sym_points,tmp) + do i=1,mo_tot_num + print *, i, real(tmp(1:3,i)) + enddo + sym_points(1,:) = -sym_points(1,:) + call compute_sym_det_values(sym_points,n_sym_points,tmp) + do i=1,n_det + print *, i, real(tmp(1:3,i)) + enddo + +end diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f new file mode 100644 index 00000000..97b7aa62 --- /dev/null +++ b/plugins/Symmetry/aos.irp.f @@ -0,0 +1,113 @@ +BEGIN_PROVIDER [ double precision, sym_box, (3,2) ] + implicit none + BEGIN_DOC + ! Opposite points of the box containing the molecule + END_DOC + integer :: i,xyz + sym_box(:,:) = 0.d0 + do xyz=1,3 + do i=1,nucl_num + sym_box(xyz,1) = min(sym_box(xyz,1), nucl_coord(i,xyz)) + sym_box(xyz,2) = max(sym_box(xyz,2), nucl_coord(i,xyz)) + enddo + enddo + sym_box(:,1) = sym_box(:,1) - 2.d0 + sym_box(:,2) = sym_box(:,2) + 2.d0 +END_PROVIDER + +subroutine generate_sym_coord(n_sym_points,result) + implicit none + integer, intent(in) :: n_sym_points + double precision, intent(out) :: result(3,n_sym_points) + BEGIN_DOC + ! xyz coordinates of points to check the symmetry, drawn uniformly in the molecular box. + END_DOC + integer :: i, xyz + + call random_number(result) + do xyz=1,3 + result(xyz,:) = sym_box(xyz,1) + result(xyz,:) * (sym_box(xyz,2)-sym_box(xyz,1)) + enddo + +end + + +subroutine compute_sym_ao_values(sym_points, n_sym_points, result) + implicit none + BEGIN_DOC + ! Values of the AO symmetry functions + END_DOC + integer, intent(in) :: n_sym_points + double precision, intent(in) :: sym_points(3,n_sym_points) + double precision, intent(out) :: result(n_sym_points, ao_num) + integer :: i, j + double precision :: x, y, z + result (:,:) = 0.d0 + do j=1,ao_num + do i=1,n_sym_points + x = sym_points(1,i) - nucl_coord_transp(1,ao_nucl(j)) + y = sym_points(2,i) - nucl_coord_transp(2,ao_nucl(j)) + z = sym_points(3,i) - nucl_coord_transp(3,ao_nucl(j)) + x = x**ao_power(j,1) + y = y**ao_power(j,2) + z = z**ao_power(j,3) + result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) + enddo + enddo + +end + +subroutine compute_sym_mo_values(sym_points, n_sym_points, result) + implicit none + BEGIN_DOC + ! Values of the MO symmetry functions + END_DOC + integer, intent(in) :: n_sym_points + double precision, intent(in) :: sym_points(3,n_sym_points) + double precision, intent(out) :: result(n_sym_points, mo_tot_num) + + double precision, allocatable :: tmp(:,:) + allocate(tmp(n_sym_points,ao_num)) + call compute_sym_ao_values(sym_points,n_sym_points,tmp) + call dgemm('N','N',n_sym_points,mo_tot_num,ao_num, & + 1.d0, tmp,size(tmp,1), mo_coef, size(mo_coef,1), & + 0.d0, result,size(result,1)) + deallocate(tmp) +end + + +subroutine compute_sym_det_values(sym_points, n_sym_points, result) + use bitmasks + implicit none + BEGIN_DOC + ! Values of the determinant symmetry functions + END_DOC + integer, intent(in) :: n_sym_points + double precision, intent(in) :: sym_points(3,n_sym_points) + double precision, intent(out) :: result(n_sym_points, N_det) + + integer :: list(N_int*bit_kind_size,2) + integer :: n_elements(2) + + integer :: i, j, imo + + double precision, allocatable :: tmp(:,:) + + allocate(tmp(n_sym_points,mo_tot_num)) + call compute_sym_mo_values(sym_points, n_sym_points, tmp) + + result = 1.d0 + do i=1,N_det + call bitstring_to_list_ab(psi_det(1,1,i), list, n_elements, N_int) + do j=1,n_elements(1) + imo = list(j,1) + result(:,i) *= tmp(:,imo) + enddo + do j=1,n_elements(2) + imo = list(j,2) + result(:,i) *= tmp(:,imo) + enddo + enddo + + deallocate(tmp) +end diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f new file mode 100644 index 00000000..4a100805 --- /dev/null +++ b/plugins/Symmetry/find_sym.irp.f @@ -0,0 +1,318 @@ +BEGIN_PROVIDER [ logical, molecule_is_linear ] + implicit none + BEGIN_DOC + ! True if the molecule is linear + END_DOC + molecule_is_linear = (minval(inertia_tensor_eigenvalues) < 1.d-5) +END_PROVIDER + +BEGIN_PROVIDER [ logical, molecule_has_center_of_inversion ] + implicit none + BEGIN_DOC + ! If true, there is a center of inversion in the WF + END_DOC + molecule_has_center_of_inversion = .True. + integer :: i,j,k + double precision :: point(3) + logical :: found + double precision, external :: u_dot_u + do i=1,nucl_num + found = .False. + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point(:) = nucl_coord_transp(:,i) + nucl_coord_transp(:,j) + if (u_dot_u(point,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + molecule_has_center_of_inversion = .False. + exit + endif + enddo + +END_PROVIDER + + +BEGIN_PROVIDER [ integer, sym_rotation_axis, (3) ] + implicit none + BEGIN_DOC + ! Order of the rotation axis + END_DOC + include 'constants.include.F' + + integer :: i,j,k + double precision :: point(3), point2(3) + logical :: found + double precision, external :: u_dot_u + integer :: iorder, iaxis + double precision :: theta, sin_t, cos_t + do iaxis=1,3 + do iorder=12,2,-1 + sym_rotation_axis(iaxis) = iorder + theta = 2.d0*pi/dble(iorder) + sin_t = dsin(theta) + cos_t = dcos(theta) + do i=1,nucl_num + found = .False. + if (iaxis==1) then + point(1) = nucl_coord_transp(1,i) + point(2) = nucl_coord_transp(2,i)*cos_t - nucl_coord_transp(3,i)*sin_t + point(3) = nucl_coord_transp(2,i)*sin_t + nucl_coord_transp(3,i)*cos_t + else if (iaxis==2) then + point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(3,i)*sin_t + point(2) = nucl_coord_transp(2,i) + point(3) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(3,i)*cos_t + endif + if (iaxis==3) then + point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(2,i)*sin_t + point(2) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(2,i)*cos_t + point(3) = nucl_coord_transp(3,i) + endif + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point2(:) = nucl_coord_transp(:,j) - point(:) + if (u_dot_u(point2,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + sym_rotation_axis(iaxis) = 1 + exit + endif + enddo + if (sym_rotation_axis(iaxis) /= 1) then + exit + endif + enddo + enddo + +END_PROVIDER + + BEGIN_PROVIDER [ integer, molecule_principal_axis ] +&BEGIN_PROVIDER [ integer, molecule_secondary_axis ] +&BEGIN_PROVIDER [ integer, molecule_ternary_axis ] + implicit none + BEGIN_DOC +! Which axis is the Z axis + END_DOC + molecule_principal_axis = maxloc(sym_rotation_axis,1) + if (molecule_principal_axis == 1) then + if (sym_rotation_axis(2) >= sym_rotation_axis(3)) then + molecule_secondary_axis = 2 + molecule_ternary_axis = 3 + else + molecule_secondary_axis = 3 + molecule_ternary_axis = 2 + endif + else if (molecule_principal_axis == 2) then + if (sym_rotation_axis(1) >= sym_rotation_axis(3)) then + molecule_secondary_axis = 1 + molecule_ternary_axis = 3 + else + molecule_secondary_axis = 3 + molecule_ternary_axis = 1 + endif + else if (molecule_principal_axis == 3) then + if (sym_rotation_axis(1) >= sym_rotation_axis(2)) then + molecule_secondary_axis = 1 + molecule_ternary_axis = 2 + else + molecule_secondary_axis = 2 + molecule_ternary_axis = 1 + endif + endif +END_PROVIDER + +BEGIN_PROVIDER [ logical, molecule_has_secondary_c2_rotation ] + implicit none + BEGIN_DOC +! If true, the molecule has a C2 rotation perpendicular to the main axis + END_DOC + if (molecule_principal_axis == 1) then + molecule_has_secondary_c2_rotation = (sym_rotation_axis(2)==2) .or. (sym_rotation_axis(3)==2) + else if (molecule_principal_axis == 2) then + molecule_has_secondary_c2_rotation = (sym_rotation_axis(1)==2) .or. (sym_rotation_axis(3)==2) + else if (molecule_principal_axis == 3) then + molecule_has_secondary_c2_rotation = (sym_rotation_axis(1)==2) .or. (sym_rotation_axis(2)==2) + endif +END_PROVIDER + + +BEGIN_PROVIDER [ logical, molecule_has_improper_rotation ] + implicit none + BEGIN_DOC + ! Order of the rotation axis + END_DOC + include 'constants.include.F' + + integer :: i,j,k + double precision :: point(3), point2(3) + logical :: found + double precision, external :: u_dot_u + integer :: iorder, iaxis + double precision :: theta, sin_t, cos_t + iaxis=molecule_principal_axis + iorder = 2*sym_rotation_axis(iaxis) + molecule_has_improper_rotation = .True. + theta = 2.d0*pi/dble(iorder) + sin_t = dsin(theta) + cos_t = dcos(theta) + do i=1,nucl_num + found = .False. + if (iaxis==1) then + point(1) = -nucl_coord_transp(1,i) + point(2) = nucl_coord_transp(2,i)*cos_t - nucl_coord_transp(3,i)*sin_t + point(3) = nucl_coord_transp(2,i)*sin_t + nucl_coord_transp(3,i)*cos_t + else if (iaxis==2) then + point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(3,i)*sin_t + point(2) = -nucl_coord_transp(2,i) + point(3) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(3,i)*cos_t + endif + if (iaxis==3) then + point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(2,i)*sin_t + point(2) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(2,i)*cos_t + point(3) = -nucl_coord_transp(3,i) + endif + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point2(:) = nucl_coord_transp(:,j) - point(:) + if (u_dot_u(point2,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + molecule_has_improper_rotation = .False. + exit + endif + enddo + +END_PROVIDER + +BEGIN_PROVIDER [ logical, molecule_has_center_of_inversion ] + implicit none + BEGIN_DOC + ! If true, there is a center of inversion in the WF + END_DOC + molecule_has_center_of_inversion = .True. + integer :: i,j,k + double precision :: point(3) + logical :: found + double precision, external :: u_dot_u + do i=1,nucl_num + found = .False. + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point(:) = nucl_coord_transp(:,i) + nucl_coord_transp(:,j) + if (u_dot_u(point,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + molecule_has_center_of_inversion = .False. + exit + endif + enddo + +END_PROVIDER + + +BEGIN_PROVIDER [ logical, molecule_has_sigma_plane, (3) ] + implicit none + BEGIN_DOC + ! If true, there is a symmetry plane perpendicular to the main axis + END_DOC + integer :: i,j,k + double precision :: point(3), point2(3) + logical :: found + double precision, external :: u_dot_u + integer :: iaxis + do iaxis=1,3 + molecule_has_sigma_plane(iaxis) = .True. + do i=1,nucl_num + found = .False. + point(:) = nucl_coord_transp(:,i) + point(iaxis) = -point(iaxis) + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point2(:) = nucl_coord_transp(:,j) - point(:) + if (u_dot_u(point2,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + molecule_has_sigma_plane(iaxis) = .False. + exit + endif + enddo + enddo + +END_PROVIDER + +subroutine find_symmetry(result) + implicit none + BEGIN_DOC +! Finds the point group of the molecule + END_DOC + character*16 :: result + character*2, save :: i_to_a(24) = (/ '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',& + '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24' /) + result = 'C1' + if (molecule_is_linear) then + if (molecule_has_center_of_inversion) then + result = 'D*h' + else + result = 'C*v' + endif + else + if (maxval(sym_rotation_axis) == 1) then + if (molecule_has_sigma_plane(1).or.molecule_has_sigma_plane(2).or.& + molecule_has_sigma_plane(3) ) then + result = 'Cs' + else + if (molecule_has_center_of_inversion) then + result = 'Ci' + endif + endif + else + if (molecule_has_secondary_c2_rotation) then + if (molecule_has_sigma_plane(molecule_principal_axis)) then + result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' + else + if (molecule_has_sigma_plane(molecule_secondary_axis)) then + result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' + else + if (molecule_has_sigma_plane(molecule_ternary_axis)) then + result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' + else + result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + endif + endif + endif + else + if (molecule_has_sigma_plane(molecule_principal_axis)) then + result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' + else + if (molecule_has_sigma_plane(molecule_secondary_axis)) then + result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' + else + if (molecule_has_sigma_plane(molecule_ternary_axis)) then + result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' + else + if (molecule_has_improper_rotation) then + result = 'S'//trim(i_to_a(2*sym_rotation_axis(molecule_principal_axis))) + else + result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + endif + endif + endif + endif + endif + endif + endif +end diff --git a/src/Nuclei/inertia.irp.f b/src/Nuclei/inertia.irp.f new file mode 100644 index 00000000..c4517cde --- /dev/null +++ b/src/Nuclei/inertia.irp.f @@ -0,0 +1,32 @@ +BEGIN_PROVIDER [ double precision, inertia_tensor, (3,3) ] + implicit none + BEGIN_DOC + ! Inertia tensor + END_DOC + integer :: i,j,k + inertia_tensor = 0.d0 + do k=1,nucl_num + inertia_tensor(1,1) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) + inertia_tensor(2,2) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) + inertia_tensor(3,3) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,2)-center_of_mass(2))**2) + inertia_tensor(1,2) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,2)-center_of_mass(2)) ) + inertia_tensor(1,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) + inertia_tensor(2,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) + enddo + inertia_tensor(2,1) = inertia_tensor(1,2) + inertia_tensor(3,1) = inertia_tensor(1,3) + inertia_tensor(3,2) = inertia_tensor(2,3) +END_PROVIDER + + BEGIN_PROVIDER [ double precision, inertia_tensor_eigenvectors, (3,3) ] +&BEGIN_PROVIDER [ double precision, inertia_tensor_eigenvalues , (3) ] + implicit none + BEGIN_DOC + ! Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation. + END_DOC + integer :: k + call lapack_diagd(inertia_tensor_eigenvalues,inertia_tensor_eigenvectors,inertia_tensor,3,3) + print *, 'Rotational constants (GHZ):' + print *, (1805.65468542d0/inertia_tensor_eigenvalues(k), k=3,1,-1) +END_PROVIDER + diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index 307a9610..43609506 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -1,4 +1,4 @@ -BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] +BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] implicit none BEGIN_DOC @@ -8,7 +8,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] if (mpi_master) then double precision, allocatable :: buffer(:,:) - nucl_coord = 0.d0 + nucl_coord_input = 0.d0 allocate (buffer(nucl_num,3)) buffer = 0.d0 logical :: has @@ -22,7 +22,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] do i=1,3 do j=1,nucl_num - nucl_coord(j,i) = buffer(j,i) + nucl_coord_input(j,i) = buffer(j,i) enddo enddo deallocate(buffer) @@ -31,6 +31,65 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' double precision, parameter :: a0= 0.529177249d0 + call write_time(output_Nuclei) + write(output_Nuclei,'(A)') '' + write(output_Nuclei,'(A)') 'Input Nuclear Coordinates (Angstroms)' + write(output_Nuclei,'(A)') '=====================================' + write(output_Nuclei,'(A)') '' + write(output_Nuclei,ft) & + '================','============','============','============','============' + write(output_Nuclei,*) & + ' Atom Charge X Y Z ' + write(output_Nuclei,ft) & + '================','============','============','============','============' + do i=1,nucl_num + write(output_Nuclei,f) nucl_label(i), nucl_charge(i), & + nucl_coord_input(i,1)*a0, & + nucl_coord_input(i,2)*a0, & + nucl_coord_input(i,3)*a0 + enddo + write(output_Nuclei,ft) & + '================','============','============','============','============' + write(output_Nuclei,'(A)') '' + + endif + + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( nucl_coord_input, 3*nucl_num, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read nucl_coord_input with MPI' + endif + IRP_ENDIF + +END_PROVIDER + +BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] + implicit none + + BEGIN_DOC + ! Nuclear coordinates in standard orientation + END_DOC + + if (mpi_master) then + integer :: i + do i=1,nucl_num + nucl_coord(i,1) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) + nucl_coord(i,2) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) + nucl_coord(i,3) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) + enddo + + character*(64), parameter :: f = '(A16, 4(1X,F12.6))' + character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' + double precision, parameter :: a0= 0.529177249d0 + call write_time(output_Nuclei) write(output_Nuclei,'(A)') '' write(output_Nuclei,'(A)') 'Nuclear Coordinates (Angstroms)' @@ -285,3 +344,87 @@ BEGIN_PROVIDER [ character*(128), element_name, (78)] element_name(78) = 'Pt' END_PROVIDER + +BEGIN_PROVIDER [ double precision, mass, (0:110) ] + implicit none + BEGIN_DOC + ! Atomic masses + END_DOC + + mass( 0 ) = 0. + mass( 1 ) = 1.0079 + mass( 2 ) = 4.00260 + mass( 3 ) = 6.941 + mass( 4 ) = 9.01218 + mass( 5 ) = 10.81 + mass( 6 ) = 12.011 + mass( 7 ) = 14.0067 + mass( 8 ) = 15.9994 + mass( 9 ) = 18.998403 + mass( 10 ) = 20.179 + mass( 11 ) = 22.98977 + mass( 12 ) = 24.305 + mass( 13 ) = 26.98154 + mass( 14 ) = 28.0855 + mass( 15 ) = 30.97376 + mass( 16 ) = 32.06 + mass( 17 ) = 35.453 + mass( 18 ) = 39.948 + mass( 19 ) = 39.0983 + mass( 20 ) = 40.08 + mass( 21 ) = 44.9559 + mass( 22 ) = 47.90 + mass( 23 ) = 50.9415 + mass( 24 ) = 51.996 + mass( 25 ) = 54.9380 + mass( 26 ) = 55.9332 + mass( 27 ) = 58.9332 + mass( 28 ) = 58.70 + mass( 29 ) = 63.546 + mass( 30 ) = 65.38 + mass( 31 ) = 69.72 + mass( 32 ) = 72.59 + mass( 33 ) = 74.9216 + mass( 34 ) = 78.96 + mass( 35 ) = 79.904 + mass( 36 ) = 83.80 + mass( 37 ) = 85.4678 + mass( 38 ) = 87.62 + mass( 39 ) = 88.90584 + mass( 40 ) = 91.224 + mass( 41 ) = 92.90637 + mass( 42 ) = 95.95 + mass( 43 ) = 98. + mass( 44 ) = 101.07 + mass( 45 ) = 102.90550 + mass( 46 ) = 106.42 + mass( 47 ) = 107.8682 + mass( 48 ) = 112.414 + mass( 49 ) = 114.818 + mass( 50 ) = 118.710 + mass( 51 ) = 121.760 + mass( 52 ) = 127.60 + mass( 53 ) = 126.90447 + mass( 54 ) = 131.293 + mass( 78 ) = 195.084 +END_PROVIDER + +BEGIN_PROVIDER [ double precision, center_of_mass, (3) ] + implicit none + BEGIN_DOC + ! Center of mass of the molecule + END_DOC + integer :: i,j + double precision :: s + center_of_mass(:) = 0.d0 + s = 0.d0 + do i=1,nucl_num + do j=1,3 + center_of_mass(j) += nucl_coord_input(i,j)* mass(int(nucl_charge(i))) + enddo + s += mass(int(nucl_charge(i))) + enddo + s = 1.d0/s + center_of_mass(:) = center_of_mass(:)*s +END_PROVIDER + From 407abf5d77cebd8448c7805232e683537f147ab9 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 15 Dec 2017 19:24:18 +0100 Subject: [PATCH 2/2] Added character tables --- data/Symmetry/C1 | 10 + data/Symmetry/C10 | 20 ++ data/Symmetry/C10h | 32 ++++ data/Symmetry/C10v | 24 +++ data/Symmetry/C11 | 20 ++ data/Symmetry/C11h | 32 ++++ data/Symmetry/C11v | 22 +++ data/Symmetry/C12 | 22 +++ data/Symmetry/C12h | 36 ++++ data/Symmetry/C12v | 26 +++ data/Symmetry/C13 | 22 +++ data/Symmetry/C13h | 36 ++++ data/Symmetry/C13v | 24 +++ data/Symmetry/C14 | 24 +++ data/Symmetry/C14h | 40 ++++ data/Symmetry/C14v | 28 +++ data/Symmetry/C15 | 24 +++ data/Symmetry/C15h | 40 ++++ data/Symmetry/C15v | 26 +++ data/Symmetry/C16 | 26 +++ data/Symmetry/C16h | 44 +++++ data/Symmetry/C16v | 30 +++ data/Symmetry/C17 | 26 +++ data/Symmetry/C17h | 44 +++++ data/Symmetry/C17v | 28 +++ data/Symmetry/C18 | 28 +++ data/Symmetry/C18h | 48 +++++ data/Symmetry/C18v | 32 ++++ data/Symmetry/C19 | 28 +++ data/Symmetry/C19h | 48 +++++ data/Symmetry/C19v | 30 +++ data/Symmetry/C1h | 12 ++ data/Symmetry/C1v | 12 ++ data/Symmetry/C2 | 12 ++ data/Symmetry/C20 | 30 +++ data/Symmetry/C20h | 52 +++++ data/Symmetry/C20v | 34 ++++ data/Symmetry/C21 | 30 +++ data/Symmetry/C21h | 52 +++++ data/Symmetry/C21v | 32 ++++ data/Symmetry/C22 | 32 ++++ data/Symmetry/C22h | 56 ++++++ data/Symmetry/C22v | 36 ++++ data/Symmetry/C23 | 32 ++++ data/Symmetry/C23h | 56 ++++++ data/Symmetry/C23v | 34 ++++ data/Symmetry/C24 | 34 ++++ data/Symmetry/C24h | 60 ++++++ data/Symmetry/C24v | 38 ++++ data/Symmetry/C25 | 34 ++++ data/Symmetry/C25h | 60 ++++++ data/Symmetry/C25v | 36 ++++ data/Symmetry/C26 | 36 ++++ data/Symmetry/C26h | 64 +++++++ data/Symmetry/C26v | 40 ++++ data/Symmetry/C27 | 36 ++++ data/Symmetry/C27h | 64 +++++++ data/Symmetry/C27v | 38 ++++ data/Symmetry/C28 | 38 ++++ data/Symmetry/C28h | 68 +++++++ data/Symmetry/C28v | 42 ++++ data/Symmetry/C29 | 38 ++++ data/Symmetry/C29h | 68 +++++++ data/Symmetry/C29v | 40 ++++ data/Symmetry/C2h | 16 ++ data/Symmetry/C2v | 16 ++ data/Symmetry/C3 | 12 ++ data/Symmetry/C30 | 40 ++++ data/Symmetry/C30h | 72 +++++++ data/Symmetry/C30v | 44 +++++ data/Symmetry/C31 | 40 ++++ data/Symmetry/C31h | 72 +++++++ data/Symmetry/C31v | 42 ++++ data/Symmetry/C32 | 42 ++++ data/Symmetry/C32h | 76 ++++++++ data/Symmetry/C32v | 46 +++++ data/Symmetry/C3h | 16 ++ data/Symmetry/C3v | 14 ++ data/Symmetry/C4 | 14 ++ data/Symmetry/C4h | 20 ++ data/Symmetry/C4v | 18 ++ data/Symmetry/C5 | 14 ++ data/Symmetry/C5h | 20 ++ data/Symmetry/C5v | 16 ++ data/Symmetry/C6 | 16 ++ data/Symmetry/C6h | 24 +++ data/Symmetry/C6v | 20 ++ data/Symmetry/C7 | 16 ++ data/Symmetry/C7h | 24 +++ data/Symmetry/C7v | 18 ++ data/Symmetry/C8 | 18 ++ data/Symmetry/C8h | 28 +++ data/Symmetry/C8v | 22 +++ data/Symmetry/C9 | 18 ++ data/Symmetry/C9h | 28 +++ data/Symmetry/C9v | 20 ++ data/Symmetry/Ci | 12 ++ data/Symmetry/Cinfv | 42 ++++ data/Symmetry/Cs | 12 ++ data/Symmetry/D1 | 12 ++ data/Symmetry/D10 | 24 +++ data/Symmetry/D10d | 34 ++++ data/Symmetry/D10h | 40 ++++ data/Symmetry/D11 | 22 +++ data/Symmetry/D11d | 36 ++++ data/Symmetry/D11h | 36 ++++ data/Symmetry/D12 | 26 +++ data/Symmetry/D12d | 38 ++++ data/Symmetry/D12h | 44 +++++ data/Symmetry/D13 | 24 +++ data/Symmetry/D13d | 40 ++++ data/Symmetry/D13h | 40 ++++ data/Symmetry/D14 | 28 +++ data/Symmetry/D14d | 42 ++++ data/Symmetry/D14h | 48 +++++ data/Symmetry/D15 | 26 +++ data/Symmetry/D15d | 44 +++++ data/Symmetry/D15h | 44 +++++ data/Symmetry/D16 | 30 +++ data/Symmetry/D16d | 46 +++++ data/Symmetry/D16h | 52 +++++ data/Symmetry/D17 | 28 +++ data/Symmetry/D17d | 48 +++++ 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68 +++++++ data/Symmetry/D28 | 42 ++++ data/Symmetry/D28d | 70 +++++++ data/Symmetry/D28h | 76 ++++++++ data/Symmetry/D29 | 40 ++++ data/Symmetry/D29d | 72 +++++++ data/Symmetry/D29h | 72 +++++++ data/Symmetry/D2d | 18 ++ data/Symmetry/D2h | 24 +++ data/Symmetry/D3 | 14 ++ data/Symmetry/D30 | 44 +++++ data/Symmetry/D30d | 74 +++++++ data/Symmetry/D30h | 80 ++++++++ data/Symmetry/D31 | 42 ++++ data/Symmetry/D31d | 76 ++++++++ data/Symmetry/D31h | 76 ++++++++ data/Symmetry/D32 | 46 +++++ data/Symmetry/D32d | 78 ++++++++ data/Symmetry/D32h | 84 ++++++++ data/Symmetry/D3d | 20 ++ data/Symmetry/D3h | 20 ++ data/Symmetry/D4 | 18 ++ data/Symmetry/D4d | 22 +++ data/Symmetry/D4h | 28 +++ data/Symmetry/D5 | 16 ++ data/Symmetry/D5d | 24 +++ data/Symmetry/D5h | 24 +++ data/Symmetry/D6 | 20 ++ data/Symmetry/D6d | 26 +++ data/Symmetry/D6h | 32 ++++ data/Symmetry/D7 | 18 ++ data/Symmetry/D7d | 28 +++ data/Symmetry/D7h | 28 +++ data/Symmetry/D8 | 22 +++ data/Symmetry/D8d | 30 +++ data/Symmetry/D8h | 36 ++++ data/Symmetry/D9 | 20 ++ data/Symmetry/D9d | 32 ++++ data/Symmetry/D9h | 32 ++++ data/Symmetry/Dinfh | 84 ++++++++ data/Symmetry/I | 18 ++ data/Symmetry/Ih | 28 +++ data/Symmetry/O | 18 ++ data/Symmetry/Oh | 28 +++ data/Symmetry/S12 | 22 +++ data/Symmetry/S16 | 26 +++ data/Symmetry/S20 | 30 +++ data/Symmetry/S24 | 34 ++++ data/Symmetry/S28 | 38 ++++ data/Symmetry/S32 | 42 ++++ data/Symmetry/S4 | 14 ++ data/Symmetry/S8 | 18 ++ data/Symmetry/T | 14 ++ data/Symmetry/Td | 18 ++ data/Symmetry/Th | 20 ++ plugins/Symmetry/Symmetry.main.irp.f | 27 +-- plugins/Symmetry/aos.irp.f | 10 +- plugins/Symmetry/find_sym.irp.f | 276 +++++++++++++++++++++------ plugins/Symmetry/sym_operation.irp.f | 77 ++++++++ scripts/utility/get_groups.py | 72 +++++++ 216 files changed, 8098 insertions(+), 82 deletions(-) create mode 100644 data/Symmetry/C1 create mode 100644 data/Symmetry/C10 create mode 100644 data/Symmetry/C10h create mode 100644 data/Symmetry/C10v create mode 100644 data/Symmetry/C11 create 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data/Symmetry/D8h create mode 100644 data/Symmetry/D9 create mode 100644 data/Symmetry/D9d create mode 100644 data/Symmetry/D9h create mode 100644 data/Symmetry/Dinfh create mode 100644 data/Symmetry/I create mode 100644 data/Symmetry/Ih create mode 100644 data/Symmetry/O create mode 100644 data/Symmetry/Oh create mode 100644 data/Symmetry/S12 create mode 100644 data/Symmetry/S16 create mode 100644 data/Symmetry/S20 create mode 100644 data/Symmetry/S24 create mode 100644 data/Symmetry/S28 create mode 100644 data/Symmetry/S32 create mode 100644 data/Symmetry/S4 create mode 100644 data/Symmetry/S8 create mode 100644 data/Symmetry/T create mode 100644 data/Symmetry/Td create mode 100644 data/Symmetry/Th create mode 100644 plugins/Symmetry/sym_operation.irp.f create mode 100755 scripts/utility/get_groups.py diff --git a/data/Symmetry/C1 b/data/Symmetry/C1 new file mode 100644 index 00000000..0cbd30c6 --- /dev/null +++ b/data/Symmetry/C1 @@ -0,0 +1,10 @@ +Group C1 +n 1 + + Irred Operation + 1 A E + +Table + 1 + 1 1.00000 + diff --git a/data/Symmetry/C10 b/data/Symmetry/C10 new file mode 100644 index 00000000..2fc79009 --- /dev/null +++ b/data/Symmetry/C10 @@ -0,0 +1,20 @@ +Group C10 +n 6 + + Irred Operation + 1 A E + 2 B C10 + 3 E1 C5 + 4 E2 C10^3 + 5 E3 C5^2 + 6 E4 C2 + +Table + 1 2 3 4 5 6 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 + 3 2.00000 1.61800 0.61800 -0.61800 -1.61800 -2.00000 + 4 2.00000 0.61800 -1.61800 -1.61800 0.61800 2.00000 + 5 2.00000 -0.61800 -1.61800 1.61800 0.61800 -2.00000 + 6 2.00000 -1.61800 0.61800 0.61800 -1.61800 2.00000 + diff --git a/data/Symmetry/C10h b/data/Symmetry/C10h new file mode 100644 index 00000000..ca22cc4a --- /dev/null +++ b/data/Symmetry/C10h @@ -0,0 +1,32 @@ +Group C10h +n 12 + + Irred Operation + 1 Ag E + 2 Bg C10 + 3 E1g C5 + 4 E2g C10^3 + 5 E3g C5^2 + 6 E4g C2 + 7 Au i + 8 Bu S10 + 9 E1u S5 + 10 E2u S10^3 + 11 E3u S5^2 + 12 E4u sh + +Table + 1 2 3 4 5 6 7 8 9 10 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2.00000 1.24698 -0.44504 -1.80194 -1.80194 -0.44504 1.24698 2.00000 1.24698 -0.44504 -1.80194 -1.80194 -0.44504 1.24698 2.00000 + 7 2.00000 0.86777 -1.24698 -1.94986 -0.44504 1.56366 1.80194 0.00000 -1.80194 -1.56366 0.44504 1.94986 1.24698 -0.86777 -2.00000 + 8 2.00000 0.44504 -1.80194 -1.24698 1.24698 1.80194 -0.44504 -2.00000 -0.44504 1.80194 1.24698 -1.24698 -1.80194 0.44504 2.00000 + 9 2.00000 0.00000 -2.00000 0.00000 2.00000 0.00000 -2.00000 0.00000 2.00000 0.00000 -2.00000 0.00000 2.00000 0.00000 -2.00000 + 10 2.00000 -0.44504 -1.80194 1.24698 1.24698 -1.80194 -0.44504 2.00000 -0.44504 -1.80194 1.24698 1.24698 -1.80194 -0.44504 2.00000 + 11 2.00000 -0.86777 -1.24698 1.94986 -0.44504 -1.56366 1.80194 0.00000 -1.80194 1.56366 0.44504 -1.94986 1.24698 0.86777 -2.00000 + 12 2.00000 -1.24698 -0.44504 1.80194 -1.80194 0.44504 1.24698 -2.00000 1.24698 0.44504 -1.80194 1.80194 -0.44504 -1.24698 2.00000 + 13 2.00000 -1.56366 0.44504 0.86777 -1.80194 1.94986 -1.24698 0.00000 1.24698 -1.94986 1.80194 -0.86777 -0.44504 1.56366 -2.00000 + 14 2.00000 -1.80194 1.24698 -0.44504 -0.44504 1.24698 -1.80194 2.00000 -1.80194 1.24698 -0.44504 -0.44504 1.24698 -1.80194 2.00000 + 15 2.00000 -1.94986 1.80194 -1.56366 1.24698 -0.86777 0.44504 0.00000 -0.44504 0.86777 -1.24698 1.56366 -1.80194 1.94986 -2.00000 + diff --git a/data/Symmetry/S32 b/data/Symmetry/S32 new file mode 100644 index 00000000..50be7a87 --- /dev/null +++ b/data/Symmetry/S32 @@ -0,0 +1,42 @@ +Group S32 +n 17 + + Irred Operation + 1 A E + 2 B S32 + 3 E1 C16 + 4 E2 S32^3 + 5 E3 C8 + 6 E4 S32^5 + 7 E5 C16^3 + 8 E6 S32^7 + 9 E7 C4 + 10 E8 S32^9 + 11 E9 C16^5 + 12 E10 S32^11 + 13 E11 C8^3 + 14 E12 S32^13 + 15 E13 C16^7 + 16 E14 S32^15 + 17 E15 C2 + +Table + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 + 3 2.00000 1.96157 1.84776 1.66294 1.41421 1.11114 0.76537 0.39018 0.00000 -0.39018 -0.76537 -1.11114 -1.41421 -1.66294 -1.84776 -1.96157 -2.00000 + 4 2.00000 1.84776 1.41421 0.76537 0.00000 -0.76537 -1.41421 -1.84776 -2.00000 -1.84776 -1.41421 -0.76537 0.00000 0.76537 1.41421 1.84776 2.00000 + 5 2.00000 1.66294 0.76537 -0.39018 -1.41421 -1.96157 -1.84776 -1.11114 0.00000 1.11114 1.84776 1.96157 1.41421 0.39018 -0.76537 -1.66294 -2.00000 + 6 2.00000 1.41421 0.00000 -1.41421 -2.00000 -1.41421 0.00000 1.41421 2.00000 1.41421 0.00000 -1.41421 -2.00000 -1.41421 0.00000 1.41421 2.00000 + 7 2.00000 1.11114 -0.76537 -1.96157 -1.41421 0.39018 1.84776 1.66294 0.00000 -1.66294 -1.84776 -0.39018 1.41421 1.96157 0.76537 -1.11114 -2.00000 + 8 2.00000 0.76537 -1.41421 -1.84776 0.00000 1.84776 1.41421 -0.76537 -2.00000 -0.76537 1.41421 1.84776 0.00000 -1.84776 -1.41421 0.76537 2.00000 + 9 2.00000 0.39018 -1.84776 -1.11114 1.41421 1.66294 -0.76537 -1.96157 0.00000 1.96157 0.76537 -1.66294 -1.41421 1.11114 1.84776 -0.39018 -2.00000 + 10 2.00000 0.00000 -2.00000 0.00000 2.00000 0.00000 -2.00000 0.00000 2.00000 0.00000 -2.00000 0.00000 2.00000 0.00000 -2.00000 0.00000 2.00000 + 11 2.00000 -0.39018 -1.84776 1.11114 1.41421 -1.66294 -0.76537 1.96157 0.00000 -1.96157 0.76537 1.66294 -1.41421 -1.11114 1.84776 0.39018 -2.00000 + 12 2.00000 -0.76537 -1.41421 1.84776 0.00000 -1.84776 1.41421 0.76537 -2.00000 0.76537 1.41421 -1.84776 0.00000 1.84776 -1.41421 -0.76537 2.00000 + 13 2.00000 -1.11114 -0.76537 1.96157 -1.41421 -0.39018 1.84776 -1.66294 0.00000 1.66294 -1.84776 0.39018 1.41421 -1.96157 0.76537 1.11114 -2.00000 + 14 2.00000 -1.41421 0.00000 1.41421 -2.00000 1.41421 0.00000 -1.41421 2.00000 -1.41421 0.00000 1.41421 -2.00000 1.41421 0.00000 -1.41421 2.00000 + 15 2.00000 -1.66294 0.76537 0.39018 -1.41421 1.96157 -1.84776 1.11114 0.00000 -1.11114 1.84776 -1.96157 1.41421 -0.39018 -0.76537 1.66294 -2.00000 + 16 2.00000 -1.84776 1.41421 -0.76537 0.00000 0.76537 -1.41421 1.84776 -2.00000 1.84776 -1.41421 0.76537 0.00000 -0.76537 1.41421 -1.84776 2.00000 + 17 2.00000 -1.96157 1.84776 -1.66294 1.41421 -1.11114 0.76537 -0.39018 0.00000 0.39018 -0.76537 1.11114 -1.41421 1.66294 -1.84776 1.96157 -2.00000 + diff --git a/data/Symmetry/S4 b/data/Symmetry/S4 new file mode 100644 index 00000000..faabefbf --- /dev/null +++ b/data/Symmetry/S4 @@ -0,0 +1,14 @@ +Group S4 +n 3 + + Irred Operation + 1 A E + 2 B S4 + 3 E C2 + +Table + 1 2 3 + 1 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 + 3 2.00000 0.00000 -2.00000 + diff --git a/data/Symmetry/S8 b/data/Symmetry/S8 new file mode 100644 index 00000000..a7a0a0e0 --- /dev/null +++ b/data/Symmetry/S8 @@ -0,0 +1,18 @@ +Group S8 +n 5 + + Irred Operation + 1 A E + 2 B S8 + 3 E1 C4 + 4 E2 S8^3 + 5 E3 C2 + +Table + 1 2 3 4 5 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 -1.00000 1.00000 + 3 2.00000 1.41420 0.00000 -1.41420 -2.00000 + 4 2.00000 0.00000 -2.00000 0.00000 2.00000 + 5 2.00000 -1.41420 0.00000 1.41420 -2.00000 + diff --git a/data/Symmetry/T b/data/Symmetry/T new file mode 100644 index 00000000..660b5106 --- /dev/null +++ b/data/Symmetry/T @@ -0,0 +1,14 @@ +Group T +n 3 + + Irred Operation + 1 A E + 2 E C3 + 3 T C2 + +Table + 1 2 3 + 1 1.00000 1.00000 1.00000 + 2 2.00000 -1.00000 2.00000 + 3 3.00000 0.00000 -1.00000 + diff --git a/data/Symmetry/Td b/data/Symmetry/Td new file mode 100644 index 00000000..bb0dbb12 --- /dev/null +++ b/data/Symmetry/Td @@ -0,0 +1,18 @@ +Group Td +n 5 + + Irred Operation + 1 A1 E + 2 A2 C3 + 3 E C2 + 4 T1 S4 + 5 T2 sd + +Table + 1 2 3 4 5 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 1.00000 1.00000 -1.00000 -1.00000 + 3 2.00000 -1.00000 2.00000 0.00000 0.00000 + 4 3.00000 0.00000 -1.00000 1.00000 -1.00000 + 5 3.00000 0.00000 -1.00000 -1.00000 1.00000 + diff --git a/data/Symmetry/Th b/data/Symmetry/Th new file mode 100644 index 00000000..06232415 --- /dev/null +++ b/data/Symmetry/Th @@ -0,0 +1,20 @@ +Group Th +n 6 + + Irred Operation + 1 Ag E + 2 Eg C3 + 3 Tg C2 + 4 Au i + 5 Eu S6 + 6 Tu sh + +Table + 1 2 3 4 5 6 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 2.00000 -1.00000 2.00000 2.00000 -1.00000 2.00000 + 3 3.00000 0.00000 -1.00000 3.00000 0.00000 -1.00000 + 4 1.00000 1.00000 1.00000 -1.00000 -1.00000 -1.00000 + 5 2.00000 -1.00000 2.00000 -2.00000 1.00000 -2.00000 + 6 3.00000 0.00000 -1.00000 -3.00000 0.00000 1.00000 + diff --git a/plugins/Symmetry/Symmetry.main.irp.f b/plugins/Symmetry/Symmetry.main.irp.f index d8d2f350..78bf126e 100644 --- a/plugins/Symmetry/Symmetry.main.irp.f +++ b/plugins/Symmetry/Symmetry.main.irp.f @@ -3,28 +3,19 @@ program Symmetry BEGIN_DOC ! TODO END_DOC - integer :: n_sym_points, i, j - double precision, allocatable :: tmp(:,:), sym_points(:,:) + integer :: i, j character*8 :: sym - n_sym_points = 3 print *, 'Molecule is linear:', molecule_is_linear print *, 'Has center of inversion:', molecule_has_center_of_inversion + print *, 'Has S2n improper rotation:', molecule_has_improper_rotation print *, 'Symmetry rotation axis:', sym_rotation_axis(:) - call find_symmetry(sym) - print *, 'Group:'//sym - return - allocate(tmp(n_sym_points,n_det), sym_points(3,n_sym_points)) - - call generate_sym_coord(n_sym_points,sym_points) - call compute_sym_det_values(sym_points,n_sym_points,tmp) - do i=1,mo_tot_num - print *, i, real(tmp(1:3,i)) + print *, 'Group:'//point_group + print *, 'Symmetry irreps', sym_irrep(1:n_irrep) + print *, 'Symmetry operations', sym_operation(1:n_irrep) + print *, 'Character table' + do i=1,n_irrep + print *, character_table(i,:) enddo - sym_points(1,:) = -sym_points(1,:) - call compute_sym_det_values(sym_points,n_sym_points,tmp) - do i=1,n_det - print *, i, real(tmp(1:3,i)) - enddo - + PROVIDE mo_sym end diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f index 97b7aa62..e4352948 100644 --- a/plugins/Symmetry/aos.irp.f +++ b/plugins/Symmetry/aos.irp.f @@ -51,7 +51,15 @@ subroutine compute_sym_ao_values(sym_points, n_sym_points, result) x = x**ao_power(j,1) y = y**ao_power(j,2) z = z**ao_power(j,3) - result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) +! result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) + result(i,j) = x*y*z + if (result(i,j) > 0.d0) then + result(i,j) = 1.d0 + else if (result(i,j) < 0.d0) then + result(i,j) = -1.d0 + else + result(i,j) = 0.d0 + endif enddo enddo diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index 4a100805..c23146c5 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -47,29 +47,12 @@ BEGIN_PROVIDER [ integer, sym_rotation_axis, (3) ] logical :: found double precision, external :: u_dot_u integer :: iorder, iaxis - double precision :: theta, sin_t, cos_t do iaxis=1,3 do iorder=12,2,-1 sym_rotation_axis(iaxis) = iorder - theta = 2.d0*pi/dble(iorder) - sin_t = dsin(theta) - cos_t = dcos(theta) do i=1,nucl_num found = .False. - if (iaxis==1) then - point(1) = nucl_coord_transp(1,i) - point(2) = nucl_coord_transp(2,i)*cos_t - nucl_coord_transp(3,i)*sin_t - point(3) = nucl_coord_transp(2,i)*sin_t + nucl_coord_transp(3,i)*cos_t - else if (iaxis==2) then - point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(3,i)*sin_t - point(2) = nucl_coord_transp(2,i) - point(3) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(3,i)*cos_t - endif - if (iaxis==3) then - point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(2,i)*sin_t - point(2) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(2,i)*cos_t - point(3) = nucl_coord_transp(3,i) - endif + call sym_apply_rotation(dble(iorder),iaxis,nucl_coord_transp(1,i),point) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle point2(:) = nucl_coord_transp(:,j) - point(:) @@ -94,6 +77,7 @@ END_PROVIDER BEGIN_PROVIDER [ integer, molecule_principal_axis ] &BEGIN_PROVIDER [ integer, molecule_secondary_axis ] &BEGIN_PROVIDER [ integer, molecule_ternary_axis ] +&BEGIN_PROVIDER [ logical, molecule_has_secondary_c2_rotation ] implicit none BEGIN_DOC ! Which axis is the Z axis @@ -124,13 +108,7 @@ END_PROVIDER molecule_ternary_axis = 1 endif endif -END_PROVIDER -BEGIN_PROVIDER [ logical, molecule_has_secondary_c2_rotation ] - implicit none - BEGIN_DOC -! If true, the molecule has a C2 rotation perpendicular to the main axis - END_DOC if (molecule_principal_axis == 1) then molecule_has_secondary_c2_rotation = (sym_rotation_axis(2)==2) .or. (sym_rotation_axis(3)==2) else if (molecule_principal_axis == 2) then @@ -138,9 +116,21 @@ BEGIN_PROVIDER [ logical, molecule_has_secondary_c2_rotation ] else if (molecule_principal_axis == 3) then molecule_has_secondary_c2_rotation = (sym_rotation_axis(1)==2) .or. (sym_rotation_axis(2)==2) endif + + if (molecule_has_secondary_c2_rotation) then + integer :: swap + if ( (sym_rotation_axis(molecule_secondary_axis) /= 2).and. & + (sym_rotation_axis(molecule_ternary_axis) == 2) ) then + swap = molecule_secondary_axis + molecule_secondary_axis = molecule_ternary_axis + molecule_ternary_axis = swap + endif + endif + END_PROVIDER + BEGIN_PROVIDER [ logical, molecule_has_improper_rotation ] implicit none BEGIN_DOC @@ -153,29 +143,12 @@ BEGIN_PROVIDER [ logical, molecule_has_improper_rotation ] logical :: found double precision, external :: u_dot_u integer :: iorder, iaxis - double precision :: theta, sin_t, cos_t iaxis=molecule_principal_axis iorder = 2*sym_rotation_axis(iaxis) molecule_has_improper_rotation = .True. - theta = 2.d0*pi/dble(iorder) - sin_t = dsin(theta) - cos_t = dcos(theta) do i=1,nucl_num found = .False. - if (iaxis==1) then - point(1) = -nucl_coord_transp(1,i) - point(2) = nucl_coord_transp(2,i)*cos_t - nucl_coord_transp(3,i)*sin_t - point(3) = nucl_coord_transp(2,i)*sin_t + nucl_coord_transp(3,i)*cos_t - else if (iaxis==2) then - point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(3,i)*sin_t - point(2) = -nucl_coord_transp(2,i) - point(3) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(3,i)*cos_t - endif - if (iaxis==3) then - point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(2,i)*sin_t - point(2) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(2,i)*cos_t - point(3) = -nucl_coord_transp(3,i) - endif + call sym_apply_improper_rotation(dble(iorder),iaxis,nucl_coord_transp(1,i),point) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle point2(:) = nucl_coord_transp(:,j) - point(:) @@ -254,60 +227,68 @@ BEGIN_PROVIDER [ logical, molecule_has_sigma_plane, (3) ] END_PROVIDER -subroutine find_symmetry(result) - implicit none - BEGIN_DOC -! Finds the point group of the molecule - END_DOC - character*16 :: result +BEGIN_PROVIDER [ character*16, point_group ] + implicit none + BEGIN_DOC +! Point group of the molecule + END_DOC + character*2, save :: i_to_a(24) = (/ '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',& '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24' /) - result = 'C1' + point_group = 'C1' if (molecule_is_linear) then if (molecule_has_center_of_inversion) then - result = 'D*h' + point_group = 'Dinfh' else - result = 'C*v' + point_group = 'Cinfv' endif else if (maxval(sym_rotation_axis) == 1) then if (molecule_has_sigma_plane(1).or.molecule_has_sigma_plane(2).or.& molecule_has_sigma_plane(3) ) then - result = 'Cs' + point_group = 'Cs' else if (molecule_has_center_of_inversion) then - result = 'Ci' + point_group = 'Ci' endif endif else if (molecule_has_secondary_c2_rotation) then if (molecule_has_sigma_plane(molecule_principal_axis)) then - result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' + point_group = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' else if (molecule_has_sigma_plane(molecule_secondary_axis)) then - result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' + point_group = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' else if (molecule_has_sigma_plane(molecule_ternary_axis)) then - result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' + point_group = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' else - result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + if ( (sym_rotation_axis(1) == 2).and. & + (sym_rotation_axis(2) == 2).and. & + (sym_rotation_axis(3) == 2).and. & + (inertia_tensor_eigenvalues(1) == inertia_tensor_eigenvalues(2)).and. & + (inertia_tensor_eigenvalues(1) == inertia_tensor_eigenvalues(3)) ) then + point_group = 'Td' + else + point_group = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + endif endif endif endif else if (molecule_has_sigma_plane(molecule_principal_axis)) then - result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' + point_group = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' else if (molecule_has_sigma_plane(molecule_secondary_axis)) then - result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' + point_group = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' else if (molecule_has_sigma_plane(molecule_ternary_axis)) then - result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' + point_group = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' else if (molecule_has_improper_rotation) then - result = 'S'//trim(i_to_a(2*sym_rotation_axis(molecule_principal_axis))) + point_group = 'S'//trim(i_to_a(2*sym_rotation_axis(molecule_principal_axis))) else - result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + point_group = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) endif endif endif @@ -315,4 +296,173 @@ subroutine find_symmetry(result) endif endif endif -end +END_PROVIDER + + +BEGIN_PROVIDER [ character*8, mo_symmetry ] + implicit none + BEGIN_DOC + ! Symmetry of the MOs + END_DOC + integer :: i,j +END_PROVIDER + + +BEGIN_PROVIDER [ integer, n_irrep ] + implicit none + BEGIN_DOC + ! Number of Irreducible representations + END_DOC + integer :: iunit, n, i + character*(256) :: qproot, buffer + integer, external :: getUnitAndOpen + call getenv('QP_ROOT',qproot) + iunit = getUnitAndOpen(trim(qproot)//'/data/Symmetry/'//trim(point_group),'r') + read(iunit,*) ! 1st line + read(iunit,*) buffer, n_irrep + close(iunit) +END_PROVIDER + + BEGIN_PROVIDER [ character*8, sym_irrep, (n_irrep) ] +&BEGIN_PROVIDER [ character*8, sym_operation, (n_irrep) ] +&BEGIN_PROVIDER [ double precision, character_table, (n_irrep,n_irrep) ] + implicit none + BEGIN_DOC + ! Irreducible representation labels, labels of symmetry operations and + ! Character table : columns are sym operations and lines are Irreps + END_DOC + integer :: iunit, n, i + character*(256) :: qproot, buffer + integer, external :: getUnitAndOpen + call getenv('QP_ROOT',qproot) + iunit = getUnitAndOpen(trim(qproot)//'/data/Symmetry/'//trim(point_group),'r') + buffer = '' + read(iunit,*) ! 1st line + read(iunit,*) buffer, n + read(iunit,*) ! empty line + read(iunit,*) ! Irred Operation + do i=1,n + read(iunit,*) buffer, sym_irrep(i), sym_operation(i) + enddo + read(iunit,*) ! empty line + read(iunit,*) ! Table + read(iunit,*) ! 1 2 3 ... + do i=1,n + read(iunit,*) buffer, character_table(i,1:n) + enddo + close(iunit) +END_PROVIDER + + +BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] + implicit none + BEGIN_DOC + ! Symmetry operations applied on MOs + END_DOC + + double precision, allocatable :: sym_points(:,:), ref_points(:,:) + double precision, allocatable :: val(:,:,:) + integer :: iangle, n_sym_points + double precision :: angle + integer :: iop, imo, ipoint, l, i + double precision :: sym_operations_on_mos(n_irrep) + logical :: possible_irrep(n_irrep,mo_tot_num) + + n_sym_points = 10000 + allocate(val(n_sym_points,mo_tot_num,2), sym_points(3,n_sym_points), ref_points(3,n_sym_points)) + + call generate_sym_coord(n_sym_points,ref_points) + call compute_sym_mo_values(ref_points,n_sym_points,val(1,1,2)) + + do iop=1,n_irrep + if (sym_operation(iop) == 'E') then + cycle + endif + possible_irrep = .True. + + if (sym_operation(iop) == 'i') then + do ipoint=1,n_sym_points + call sym_apply_inversion(ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'sh') then + do ipoint=1,n_sym_points + call sym_apply_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 's') then + do ipoint=1,n_sym_points + call sym_apply_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'sv') then + do ipoint=1,n_sym_points + call sym_apply_reflexion(molecule_secondary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'sd') then + do ipoint=1,n_sym_points + call sym_apply_diagonal_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'C2''') then + do ipoint=1,n_sym_points + call sym_apply_rotation(angle,molecule_secondary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'C2"') then + do ipoint=1,n_sym_points + call sym_apply_rotation(angle,molecule_ternary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else + do l=2,len(sym_operation(iop)) + if (sym_operation(iop)(l:l) == '^') exit + enddo + read(sym_operation(iop)(2:l-1), *) iangle + l=1 + read(sym_operation(iop)(l+1:), *, err=10, end=10) l + 10 continue + angle = dble(iangle)/(dble(l)) + if (sym_operation(iop)(1:1) == 'C') then + do ipoint=1,n_sym_points + call sym_apply_rotation(angle,molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop)(1:1) == 'S') then + do ipoint=1,n_sym_points + call sym_apply_improper_rotation(angle,molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + endif + endif + + call compute_sym_mo_values(sym_points,n_sym_points,val(1,1,1)) + + print *, sym_operation(iop) + do imo=1,mo_tot_num + sym_operations_on_mos(imo) = 0.d0 + do ipoint=1,n_sym_points + double precision :: x + x = val(ipoint,imo,1)/val(ipoint,imo,2) + if (dabs(x) > 1.d0) then + x = 1.d0/x + endif + sym_operations_on_mos(imo) += x + enddo + sym_operations_on_mos(imo) *= 1.d0/n_sym_points + if (dabs(sym_operations_on_mos(imo)-1.d0) < 1.d-2) then + sym_operations_on_mos(imo)=1.d0 + else if (dabs(sym_operations_on_mos(imo)+1.d0) < 1.d-2) then + sym_operations_on_mos(imo)=-1.d0 + endif + do i=1,n_irrep + if (character_table(i,iop) /= sym_operations_on_mos(imo)) then + possible_irrep(i,imo) = .False. + endif + enddo + enddo + enddo + do imo=1,mo_tot_num + print *, imo + do i=1,n_irrep + if (possible_irrep(i,imo)) then + print *, sym_irrep(i) + endif + enddo + print *, '' + enddo + +END_PROVIDER + diff --git a/plugins/Symmetry/sym_operation.irp.f b/plugins/Symmetry/sym_operation.irp.f new file mode 100644 index 00000000..93e580e2 --- /dev/null +++ b/plugins/Symmetry/sym_operation.irp.f @@ -0,0 +1,77 @@ +subroutine sym_apply_inversion(point_in, point_out) + implicit none + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + point_out(:) = -point_in(:) +end + +subroutine sym_apply_reflexion(iaxis,point_in,point_out) + implicit none + integer, intent(in) :: iaxis + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + point_out(:) = point_in(:) + point_out(iaxis) = -point_in(iaxis) + +end + +subroutine sym_apply_diagonal_reflexion(iaxis,point_in,point_out) + implicit none + integer, intent(in) :: iaxis + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + if (iaxis == 1) then + point_out(1) = point_in(1) + point_out(2) = point_in(3) + point_out(3) = point_in(2) + else if (iaxis == 2) then + point_out(1) = point_in(3) + point_out(2) = point_in(2) + point_out(3) = point_in(1) + else if (iaxis == 3) then + point_out(1) = point_in(2) + point_out(2) = point_in(1) + point_out(3) = point_in(3) + endif + +end + +subroutine sym_apply_rotation(angle,iaxis,point_in,point_out) + implicit none + double precision, intent(in) :: angle + integer, intent(in) :: iaxis + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + double precision :: theta, sin_t, cos_t + double precision, parameter :: pi = dacos(-1.d0) + theta = 2.d0*pi/angle + sin_t = dsin(theta) + cos_t = dcos(theta) + if (iaxis==1) then + point_out(1) = point_in(1) + point_out(2) = point_in(2)*cos_t - point_in(3)*sin_t + point_out(3) = point_in(2)*sin_t + point_in(3)*cos_t + else if (iaxis==2) then + point_out(1) = point_in(1)*cos_t - point_in(3)*sin_t + point_out(2) = point_in(2) + point_out(3) = point_in(1)*sin_t + point_in(3)*cos_t + endif + if (iaxis==3) then + point_out(1) = point_in(1)*cos_t - point_in(2)*sin_t + point_out(2) = point_in(1)*sin_t + point_in(2)*cos_t + point_out(3) = point_in(3) + endif +end + +subroutine sym_apply_improper_rotation(angle,iaxis,point_in,point_out) + implicit none + double precision, intent(in) :: angle + integer, intent(in) :: iaxis + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + double precision :: point_tmp(3) + call sym_apply_rotation(angle,iaxis,point_in,point_tmp) + call sym_apply_reflexion(iaxis,point_tmp,point_out) +end + + diff --git a/scripts/utility/get_groups.py b/scripts/utility/get_groups.py new file mode 100755 index 00000000..e8a24d84 --- /dev/null +++ b/scripts/utility/get_groups.py @@ -0,0 +1,72 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import urllib +import sys +from bs4 import BeautifulSoup + +address="http://gernot-katzers-spice-pages.com/character_tables/%s.html?fmt=simple" + +def clean_up(text): + soup = BeautifulSoup(text, "lxml") + pre = soup.pre + group = pre.b.get_text() + sop = {} + irred = {} + irred_count = 0 + sop_count = 0 + for span in pre.find_all('span'): + cls = span.get('class') + if cls == ['sop']: + a = span.decode_contents() + if a not in sop: + sop[a] = sop_count + sop_count += 1 + elif cls == ['irred']: + a = span.decode_contents() + if a not in irred: + irred[a] = irred_count + irred_count += 1 + table = [ [] for j in sop ] + data = pre.get_text().splitlines() + def f(x): + y = x.split() + if len(y) == 0: + return False + else: + return y[0] in irred + data = filter(f,data)[:len(irred)] + for line in data: + s = line.replace('*','').split() + l = irred[s[0]] + data[l] = map(float,s[1:len(irred)+1]) + + d = {} + e = {} + for k in irred: + d[irred[k]] = k + for k in sop: + e[sop[k]] = k + n = len(irred) + print "Group\t", group, "\nn\t", n + print "\n \tIrred \tOperation" + for i in range(n): + print "%4d \t %s \t %s"%(i+1, d[i].ljust(10), e[i].ljust(10)) + + print "\nTable\n ", + for j in range(n): + print "%8s "%(str(j+1).center(8)), + for i in range(n): + print "\n%4d "%(i+1), + for j in range(n): + print "%8.5f "%(data[i][j]), + print "\n" + +def main(): + for group in sys.argv[1:]: + f = urllib.urlopen(address%(group)) + html = f.read().split('\n',1)[1] + text = clean_up(html) + +if __name__ == "__main__": + main()