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At gaussian wt post mpi #3

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At gaussian wt post mpi #3

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d558e03
moved changes here
gelzinyte Jun 6, 2022
026abcb
made into pointer
gelzinyte Jun 6, 2022
d3702c3
space-string instead of empty string
gelzinyte Jun 6, 2022
60108c0
added has_value_target
gelzinyte Jun 6, 2022
bfbb77d
seems to compile ok
gelzinyte Jun 14, 2022
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37 changes: 37 additions & 0 deletions descriptors.f95
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Original file line number Diff line number Diff line change
Expand Up @@ -7140,6 +7140,11 @@ subroutine soap_calc(this,at,descriptor_out,do_descriptor,do_grad_descriptor,arg
complex(dp), allocatable, save :: sphericalycartesian_all_t(:,:), gradsphericalycartesian_all_t(:,:,:)
complex(dp) :: c_tmp(3)
integer :: max_n_neigh

character(len=STRING_LENGTH) :: atom_gaussian_weight_name
real(dp), dimension(:), pointer :: atom_gaussian_weight_pointer
logical :: has_atom_gaussian_weight_name

!$omp threadprivate(radial_fun, radial_coefficient, grad_radial_fun, grad_radial_coefficient)
!$omp threadprivate(sphericalycartesian_all_t, gradsphericalycartesian_all_t)
!$omp threadprivate(fourier_so3_r, fourier_so3_i)
Expand Down Expand Up @@ -7172,6 +7177,10 @@ subroutine soap_calc(this,at,descriptor_out,do_descriptor,do_grad_descriptor,arg
has_atom_mask_name = .false. ! allow atom mask column in the atom table
atom_mask_pointer => null() ! allow atom mask column in the atom table
xml_version = 1423143769 ! This is the version number where the 2l+1 normalisation of soap vectors was introduced

has_atom_gaussian_weight_name = .false.
atom_gaussian_weight_pointer => null()

if(present(args_str)) then
call initialise(params)

Expand All @@ -7182,6 +7191,10 @@ subroutine soap_calc(this,at,descriptor_out,do_descriptor,do_grad_descriptor,arg
call param_register(params, 'xml_version', '1423143769', xml_version, &
help_string="Version of GAP the XML potential file was created")

call param_register(params, 'atom_gaussian_weight_name', 'NONE', atom_gaussian_weight_name, &
has_value_target=has_atom_gaussian_weight_name, &
help_string="Array name from which to read prefactor for atom gaussians in the atomic neighbourhood density")

if (.not. param_read_line(params,args_str,ignore_unknown=.true.,task='soap_calc args_str')) then
RAISE_ERROR("soap_calc failed to parse args_str='"//trim(args_str)//"'", error)
endif
Expand All @@ -7196,6 +7209,17 @@ subroutine soap_calc(this,at,descriptor_out,do_descriptor,do_grad_descriptor,arg
atom_mask_pointer => null()
endif

if( has_atom_gaussian_weight_name ) then
if (.not. assign_pointer(at, trim(atom_gaussian_weight_name), atom_gaussian_weight_pointer)) then
RAISE_ERROR("soap_calc did not find "//trim(atom_gaussian_weight_name)//" property in the atoms object.", error)
endif
call print("got atom gaussian weight")
else
atom_mask_pointer => null() ! this would have been null anyway, so why to reassign it to null?
call print("DID NOT get atom gaussian weight")

endif

endif

if( this%cutoff_dexp > 0 ) then
Expand Down Expand Up @@ -7396,8 +7420,10 @@ subroutine soap_calc(this,at,descriptor_out,do_descriptor,do_grad_descriptor,arg
global_fourier_so3_i_array = 0.0_dp
endif ! this%global

! not sure if "atom_gaussian_weight_pointer has to be shared or if that's what messes things up?
!$omp parallel do schedule(dynamic) default(none) shared(this, at, descriptor_out, my_do_descriptor, my_do_grad_descriptor, d, i_desc, species_map, rs_index, do_two_l_plus_one) &
!$omp shared(global_grad_fourier_so3_r_array, global_grad_fourier_so3_i_array, norm_radial_decay) &
!$omp shared(atom_gaussian_weight_pointer) &
!$omp private(i, j, i_species, j_species, a, b, l, m, n, n_i, r_ij, u_ij, d_ij, shift_ij, i_pow, i_coeff, ia, jb, alpha, i_desc_i) &
!$omp private(c_tmp) &
!$omp private(t_g_r, t_g_i, t_f_r, t_f_i, t_g_f_rr, t_g_f_ii) &
Expand Down Expand Up @@ -7438,6 +7464,12 @@ subroutine soap_calc(this,at,descriptor_out,do_descriptor,do_grad_descriptor,arg
if( this%central_reference_all_species .or. this%species_Z(i_species) == at%Z(i) .or. this%species_Z(i_species) == 0 ) then
fourier_so3_r(0,a,i_species)%m(0) = this%central_weight * real(radial_coefficient(0,a) * SphericalYCartesian(0,0,(/0.0_dp, 0.0_dp, 0.0_dp/)), dp)
fourier_so3_i(0,a,i_species)%m(0) = this%central_weight * aimag(radial_coefficient(0,a) * SphericalYCartesian(0,0,(/0.0_dp, 0.0_dp, 0.0_dp/)))

if(associated(atom_gaussian_weight_pointer)) then
fourier_so3_r(0,a,i_species)%m(0) = fourier_so3_r(0,a,i_species)%m(0) * atom_gaussian_weight_pointer(i)
fourier_so3_i(0,a,i_species)%m(0) = fourier_so3_i(0,a,i_species)%m(0) * atom_gaussian_weight_pointer(i)
endif

else
fourier_so3_i(0,a,i_species)%m(0) = 0.0_dp
fourier_so3_r(0,a,i_species)%m(0) = 0.0_dp
Expand Down Expand Up @@ -7482,6 +7514,11 @@ subroutine soap_calc(this,at,descriptor_out,do_descriptor,do_grad_descriptor,arg
endif
f_cut = f_cut * radial_decay

if(associated(atom_gaussian_weight_pointer)) then
f_cut = f_cut * atom_gaussian_weight_pointer(j)
df_cut = df_cut * atom_gaussian_weight_pointer(j)
endif

do a = 1, this%n_max
arg_bess = 2.0_dp * this%alpha * r_ij * this%r_basis(a)
exp_p = exp( -this%alpha*( r_ij + this%r_basis(a) )**2 )
Expand Down
19 changes: 17 additions & 2 deletions gap_fit_module.f95
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,8 @@ module gap_fit_module
logical :: sparse_use_actual_gpcov
logical :: has_template_file, has_e0, has_local_property0, has_e0_offset, has_linear_system_dump_file

character(len=STRING_LENGTH) :: descriptor_args_str

endtype gap_fit

private
Expand Down Expand Up @@ -180,6 +182,12 @@ subroutine gap_fit_parse_command_line(this)
integer :: rnd_seed
integer, pointer :: mpi_blocksize

! this was the bug, I think
! character(len=STRING_LENGTH) :: descriptor_args_str
character(len=STRING_LENGTH), pointer :: descriptor_args_str
logical :: has_descriptor_args_str


config_file => this%config_file
at_file => this%at_file
e0_str => this%e0_str
Expand Down Expand Up @@ -208,6 +216,8 @@ subroutine gap_fit_parse_command_line(this)
gp_file => this%gp_file
template_file => this%template_file
sparsify_only_no_fit => this%sparsify_only_no_fit
descriptor_args_str => this%descriptor_args_str

condition_number_norm => this%condition_number_norm
linear_system_dump_file => this%linear_system_dump_file
mpi_blocksize => this%mpi_blocksize
Expand Down Expand Up @@ -331,9 +341,12 @@ subroutine gap_fit_parse_command_line(this)
call param_register(params, 'template_file', 'template.xyz', template_file, has_value_target=this%has_template_file, &
help_string="Template XYZ file for initialising object")

call param_register(params, 'descriptor_args_str', '', descriptor_args_str, &
help_string="Arguments string for descriptor")

call param_register(params, 'sparsify_only_no_fit', 'F', sparsify_only_no_fit, &
help_string="If true, sparsification is done, but no fitting. print the sparse index by adding print_sparse_index=file.dat to the descriptor string.")

call param_register(params, 'condition_number_norm', ' ', condition_number_norm, &
help_string="Norm for condition number of matrix A; O: 1-norm, I: inf-norm, <space>: skip calculation (default)")

Expand Down Expand Up @@ -1217,7 +1230,9 @@ subroutine fit_data_from_xyz(this,error)
do i_coordinate = 1, this%n_coordinate

call calc(this%my_descriptor(i_coordinate),this%at(n_con),my_descriptor_data, &
do_descriptor=.true.,do_grad_descriptor=has_force .or. has_virial)
do_descriptor=.true.,do_grad_descriptor=has_force .or. has_virial, args_str=this%descriptor_args_str)
! old: check this if doesn't work
! do_descriptor=.true.,do_grad_descriptor=has_force .or. has_virial)

allocate(xloc(size(my_descriptor_data%x)))
n_descriptors = n_descriptors + size(my_descriptor_data%x)
Expand Down