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Merge branch 'dev-stable' of https://github.com/QuantumPackage/qp2 into dev-stable

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eginer 2024-02-29 18:44:51 +01:00
commit 099645e3fb
12 changed files with 97 additions and 87 deletions
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8
bin/qp_convert_output_to_ezfio
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@ -224,14 +224,18 @@ def write_ezfio(res, filename):
exponent += [p.expo for p in b.prim]
ang_mom.append(str.count(s, "z"))
shell_prim_num.append(len(b.prim))
shell_index += [nshell_tot+1] * len(b.prim)
shell_index += [nshell_tot] * len(b.prim)
shell_num = len(ang_mom)
assert(shell_index[0] = 1)
assert(shell_index[-1] = shell_num)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_basis_basis("Read from ResultsFile")
ezfio.set_basis_shell_num(len(ang_mom))
ezfio.set_basis_shell_num(shell_num)
ezfio.set_basis_basis_nucleus_index(nucl_index)
ezfio.set_basis_prim_num(len(coefficient))

3
ocaml/Angmom.ml
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@ -26,8 +26,7 @@ let of_string = function
| "J" | "j" -> J
| "K" | "k" -> K
| "L" | "l" -> L
| x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L,
not "^x^"."))
| x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L, not "^x^"."))
let of_char = function
| 'S' | 's' -> S

2
ocaml/Basis.ml
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@ -17,7 +17,7 @@ let read in_channel at_number =
(** Find an element in the basis set file *)
let find in_channel element =
seek_in in_channel 0;
let element_read = ref Element.X in
let element_read = ref Element.Og in
while !element_read <> element
do
let buffer = input_line in_channel in

38
ocaml/Element.ml
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@ -4,7 +4,7 @@ open Qptypes
exception ElementError of string
type t = X
|H |He
|Li|Be |B |C |N |O |F |Ne
|Na|Mg |Al|Si|P |S |Cl|Ar
@ -20,7 +20,7 @@ type t = X
let of_string x =
match (String.capitalize_ascii (String.lowercase_ascii x)) with
| "X" | "Dummy" -> X
| "X" | "Ghost" -> X
| "H" | "Hydrogen" -> H
| "He" | "Helium" -> He
| "Li" | "Lithium" -> Li
@ -265,7 +265,7 @@ let to_string = function
let to_long_string = function
| X -> "Dummy"
| X -> "Ghost"
| H -> "Hydrogen"
| He -> "Helium"
| Li -> "Lithium"
@ -492,20 +492,20 @@ let to_charge c =
| No -> 102
| Lr -> 103
| Rf -> 104
| Db -> 105
| Sg -> 106
| Bh -> 107
| Hs -> 108
| Mt -> 109
| Ds -> 110
| Rg -> 111
| Cn -> 112
| Nh -> 113
| Fl -> 114
| Mc -> 115
| Lv -> 116
| Ts -> 117
| Og -> 118
| Db -> 105
| Sg -> 106
| Bh -> 107
| Hs -> 108
| Mt -> 109
| Ds -> 110
| Rg -> 111
| Cn -> 112
| Nh -> 113
| Fl -> 114
| Mc -> 115
| Lv -> 116
| Ts -> 117
| Og -> 118
in Charge.of_int result
@ -565,7 +565,7 @@ let of_charge c = match (Charge.to_int c) with
| 52 -> Te
| 53 -> I
| 54 -> Xe
| 55 -> Cs
| 55 -> Cs
| 56 -> Ba
| 57 -> La
| 58 -> Ce
@ -880,7 +880,7 @@ let vdw_radius x =
| Ts -> None
| Og -> None
in
match result x with
match result x with
| Some y -> Some (Positive_float.of_float @@ Units.angstrom_to_bohr *. y )
| None -> None

42
ocaml/qp_create_ezfio.ml
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@ -6,8 +6,8 @@ type element =
| Element of Element.t
| Int_elem of (Nucl_number.t * Element.t)
(** Handle dummy atoms placed on bonds *)
let dummy_centers ~threshold ~molecule ~nuclei =
(** Handle ghost atoms placed on bonds *)
let ghost_centers ~threshold ~molecule ~nuclei =
let d =
Molecule.distance_matrix molecule
in
@ -68,11 +68,11 @@ let run ?o b au c d m p cart xyz_file =
(Molecule.of_file xyz_file ~charge:(Charge.of_int c)
~multiplicity:(Multiplicity.of_int m) )
in
let dummy =
dummy_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
let ghost =
ghost_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
in
let nuclei =
molecule.Molecule.nuclei @ dummy
molecule.Molecule.nuclei @ ghost
in
@ -145,8 +145,6 @@ let run ?o b au c d m p cart xyz_file =
| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
| _ -> failwith "Expected format is int,Element:basis"
in Int_elem result
and basis =
String.lowercase_ascii basis
in
let key =
match elem with
@ -313,7 +311,7 @@ let run ?o b au c d m p cart xyz_file =
}
in
let nuclei =
molecule.Molecule.nuclei @ dummy
molecule.Molecule.nuclei @ ghost
in
@ -491,11 +489,7 @@ let run ?o b au c d m p cart xyz_file =
|> List.rev
|> list_map (fun (x,i) ->
try
let e =
match x.Atom.element with
| Element.X -> Element.H
| e -> e
in
let e = x.Atom.element in
let key =
Int_elem (i,x.Atom.element)
in
@ -507,9 +501,15 @@ let run ?o b au c d m p cart xyz_file =
in
try
Basis.read_element (basis_channel key) i e
with Not_found ->
failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
(Element.to_string x.Atom.element) )
with _ ->
try
if e = Element.X then
Basis.read_element (basis_channel key) i (Element.H)
else
raise Not_found
with Not_found ->
failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
(Element.to_string x.Atom.element) )
with
| End_of_file -> failwith
("Element "^(Element.to_string x.Atom.element)^" not found in basis set.")
@ -710,9 +710,9 @@ If a file with the same name as the basis set exists, this file will be read. O
arg=With_arg "<int>";
doc="Total charge of the molecule. Default is 0. For negative values, use m instead of -, for ex m1"} ;
{ opt=Optional ; short='d'; long="dummy";
{ opt=Optional ; short='g'; long="ghost";
arg=With_arg "<float>";
doc="Add dummy atoms. x * (covalent radii of the atoms)."} ;
doc="Add ghost atoms. x * (covalent radii of the atoms)."} ;
{ opt=Optional ; short='m'; long="multiplicity";
arg=With_arg "<int>";
@ -756,8 +756,8 @@ If a file with the same name as the basis set exists, this file will be read. O
int_of_string x )
in
let dummy =
match Command_line.get "dummy" with
let ghost =
match Command_line.get "ghost" with
| None -> 0.
| Some x -> float_of_string x
in
@ -782,7 +782,7 @@ If a file with the same name as the basis set exists, this file will be read. O
| x::_ -> x
in
run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename
run ?o:output basis au charge ghost multiplicity pseudo cart xyz_filename
)
with
(* | Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt *)

45
plugins/local/cipsi_tc_bi_ortho/run_pt2_slave.irp.f
View File

@ -31,11 +31,12 @@ subroutine run_pt2_slave(thread,iproc,energy)
double precision, intent(in) :: energy(N_states_diag)
integer, intent(in) :: thread, iproc
if (N_det > 100000 ) then
call run_pt2_slave_large(thread,iproc,energy)
else
call run_pt2_slave_small(thread,iproc,energy)
endif
call run_pt2_slave_large(thread,iproc,energy)
! if (N_det > 100000 ) then
! call run_pt2_slave_large(thread,iproc,energy)
! else
! call run_pt2_slave_small(thread,iproc,energy)
! endif
end
subroutine run_pt2_slave_small(thread,iproc,energy)
@ -178,15 +179,12 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
type(pt2_type) :: pt2_data
integer :: n_tasks, k, N
integer :: i_generator, subset
integer :: ifirst
integer :: bsize ! Size of selection buffers
logical :: sending
double precision :: time_shift
PROVIDE global_selection_buffer global_selection_buffer_lock
call random_number(time_shift)
time_shift = time_shift*15.d0
zmq_to_qp_run_socket = new_zmq_to_qp_run_socket()
@ -198,15 +196,13 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
zmq_socket_push = new_zmq_push_socket(thread)
ifirst = 0
b%N = 0
buffer_ready = .False.
n_tasks = 1
sending = .False.
done = .False.
double precision :: time0, time1
call wall_time(time0)
time0 = time0+time_shift
do while (.not.done)
integer, external :: get_tasks_from_taskserver
@ -233,28 +229,29 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
ASSERT (b%N == bsize)
endif
double precision :: time0, time1
call wall_time(time0)
call pt2_alloc(pt2_data,N_states)
b%cur = 0
call select_connected(i_generator,energy,pt2_data,b,subset,pt2_F(i_generator))
call wall_time(time1)
integer, external :: tasks_done_to_taskserver
if (tasks_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id,n_tasks) == -1) then
done = .true.
endif
call sort_selection_buffer(b)
call wall_time(time1)
! if (time1-time0 > 15.d0) then
call omp_set_lock(global_selection_buffer_lock)
global_selection_buffer%mini = b%mini
call merge_selection_buffers(b,global_selection_buffer)
b%cur=0
call omp_unset_lock(global_selection_buffer_lock)
call wall_time(time0)
! endif
call push_pt2_results_async_recv(zmq_socket_push,b%mini,sending)
if ( iproc == 1 .or. i_generator < 100 .or. done) then
call omp_set_lock(global_selection_buffer_lock)
global_selection_buffer%mini = b%mini
call merge_selection_buffers(b,global_selection_buffer)
if (ifirst /= 0 ) then
b%cur=0
else
ifirst = 1
endif
call omp_unset_lock(global_selection_buffer_lock)
if ( iproc == 1 ) then
call omp_set_lock(global_selection_buffer_lock)
call push_pt2_results_async_send(zmq_socket_push, (/i_generator/), (/pt2_data/), global_selection_buffer, (/task_id/), 1,sending)
global_selection_buffer%cur = 0

29
plugins/local/cipsi_tc_bi_ortho/run_selection_slave.irp.f
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@ -5,19 +5,22 @@ subroutine run_selection_slave(thread, iproc, energy)
implicit none
double precision, intent(in) :: energy(N_states)
integer, intent(in) :: thread, iproc
double precision, intent(in) :: energy(N_states)
integer, intent(in) :: thread, iproc
integer :: rc, i
integer :: rc, i
integer :: worker_id, task_id(1), ctask, ltask
character*(512) :: task
integer(ZMQ_PTR) :: zmq_to_qp_run_socket
integer(ZMQ_PTR) :: zmq_socket_push
integer(ZMQ_PTR), external :: new_zmq_to_qp_run_socket
integer(ZMQ_PTR), external :: new_zmq_push_socket
type(selection_buffer) :: buf, buf2
type(pt2_type) :: pt2_data
logical :: done, buffer_ready
integer :: worker_id, task_id(1), ctask, ltask
character*(512) :: task
integer(ZMQ_PTR),external :: new_zmq_to_qp_run_socket
integer(ZMQ_PTR) :: zmq_to_qp_run_socket
integer(ZMQ_PTR), external :: new_zmq_push_socket
integer(ZMQ_PTR) :: zmq_socket_push
type(selection_buffer) :: buf, buf2
logical :: done, buffer_ready
type(pt2_type) :: pt2_data
PROVIDE psi_bilinear_matrix_columns_loc psi_det_alpha_unique psi_det_beta_unique
PROVIDE psi_bilinear_matrix_rows psi_det_sorted_tc_order psi_bilinear_matrix_order
@ -64,7 +67,7 @@ subroutine run_selection_slave(thread, iproc, energy)
stop '-1'
end if
end if
call select_connected(i_generator, energy, pt2_data, buf,subset, pt2_F(i_generator))
call select_connected(i_generator, energy, pt2_data, buf, subset, pt2_F(i_generator))
endif
integer, external :: task_done_to_taskserver

3
plugins/local/cipsi_tc_bi_ortho/zmq_selection.irp.f
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@ -11,7 +11,7 @@ subroutine ZMQ_selection(N_in, pt2_data)
integer, external :: omp_get_thread_num
type(pt2_type), intent(inout) :: pt2_data
PROVIDE psi_det psi_coef N_det qp_max_mem N_states pt2_F s2_eig N_det_generators
! PROVIDE psi_det psi_coef N_det qp_max_mem N_states pt2_F s2_eig N_det_generators
N = max(N_in,1)
N = min(N, (elec_alpha_num * (mo_num-elec_alpha_num))**2)
@ -61,7 +61,6 @@ subroutine ZMQ_selection(N_in, pt2_data)
ipos=1
task = ' '
do i= 1, N_det_generators
do j=1,pt2_F(i)
write(task(ipos:ipos+30),'(I9,1X,I9,1X,I9,''|'')') j, i, N

8
src/cipsi/run_pt2_slave.irp.f
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@ -186,6 +186,7 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
type(pt2_type) :: pt2_data
integer :: n_tasks, k, N
integer :: i_generator, subset
integer :: ifirst
integer :: bsize ! Size of selection buffers
logical :: sending
@ -202,6 +203,7 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
zmq_socket_push = new_zmq_push_socket(thread)
ifirst = 0
b%N = 0
buffer_ready = .False.
n_tasks = 1
@ -250,7 +252,11 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
call omp_set_lock(global_selection_buffer_lock)
global_selection_buffer%mini = b%mini
call merge_selection_buffers(b,global_selection_buffer)
b%cur=0
if (ifirst /= 0 ) then
b%cur=0
else
ifirst = 1
endif
call omp_unset_lock(global_selection_buffer_lock)
if ( iproc == 1 ) then
call omp_set_lock(global_selection_buffer_lock)

2
src/cipsi/run_selection_slave.irp.f
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@ -65,7 +65,7 @@ subroutine run_selection_slave(thread,iproc,energy)
stop '-1'
end if
end if
call select_connected(i_generator,energy,pt2_data,buf,subset,pt2_F(i_generator))
call select_connected(i_generator, energy, pt2_data, buf, subset, pt2_F(i_generator))
endif
integer, external :: task_done_to_taskserver

1
src/tools/diagonalize_h.irp.f
View File

@ -20,4 +20,5 @@ subroutine routine
call diagonalize_CI
print*,'N_det = ',N_det
call save_wavefunction_general(N_det,N_states,psi_det_sorted,size(psi_coef_sorted,1),psi_coef_sorted)
call print_mol_properties
end

3
src/tools/print_energy.irp.f
View File

@ -14,5 +14,6 @@ end
subroutine run
implicit none
print *, psi_energy + nuclear_repulsion
call print_mol_properties
print *, psi_energy + nuclear_repulsion
end