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Fixes for numerical orbitals in qp_import
continuous-integration/drone/push Build is failing Details

This commit is contained in:
Anthony Scemama 2023-05-30 13:48:34 +02:00
parent 5817bbf573
commit f0ad63966a
4 changed files with 236 additions and 98 deletions
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47
ocaml/Input_ao_basis.ml
View File

@ -44,8 +44,12 @@ end = struct
let get_default = Qpackage.get_ezfio_default "ao_basis";;
let read_ao_basis () =
Ezfio.get_ao_basis_ao_basis ()
|> AO_basis_name.of_string
let result =
Ezfio.get_ao_basis_ao_basis ()
in
if result <> "None" then
AO_basis_name.of_string result
else failwith "No basis"
;;
let read_ao_num () =
@ -192,7 +196,7 @@ end = struct
ao_expo ;
ao_cartesian ;
ao_normalized ;
primitives_normalized ;
primitives_normalized ;
} = b
in
write_md5 b ;
@ -207,7 +211,7 @@ end = struct
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
let ao_nucl =
let ao_nucl =
Array.to_list ao_nucl
|> list_map Nucl_number.to_int
in
@ -215,7 +219,7 @@ end = struct
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
let ao_power =
let l = Array.to_list ao_power in
let l = Array.to_list ao_power in
List.concat [
(list_map (fun a -> Positive_int.to_int a.Angmom.Xyz.x) l) ;
(list_map (fun a -> Positive_int.to_int a.Angmom.Xyz.y) l) ;
@ -227,7 +231,7 @@ end = struct
Ezfio.set_ao_basis_ao_cartesian(ao_cartesian);
Ezfio.set_ao_basis_ao_normalized(ao_normalized);
Ezfio.set_ao_basis_primitives_normalized(primitives_normalized);
let ao_coef =
Array.to_list ao_coef
|> list_map AO_coef.to_float
@ -267,7 +271,10 @@ end = struct
|> Ezfio.set_ao_basis_ao_md5 ;
Some result
with
| _ -> (Ezfio.set_ao_basis_ao_md5 "None" ; None)
| _ -> ( "None"
|> Digest.string
|> Digest.to_hex
|> Ezfio.set_ao_basis_ao_md5 ; None)
;;
@ -276,7 +283,7 @@ end = struct
to_basis b
|> Long_basis.of_basis
|> Array.of_list
and unordered_basis =
and unordered_basis =
to_long_basis b
|> Array.of_list
in
@ -289,15 +296,15 @@ end = struct
(a.(i) <- None ; i)
else
find x a (i+1)
and find2 (s,g,n) a i =
and find2 (s,g,n) a i =
if i = Array.length a then -1
else
match a.(i) with
match a.(i) with
| None -> find2 (s,g,n) a (i+1)
| Some (s', g', n') ->
if s <> s' || n <> n' then find2 (s,g,n) a (i+1)
else
let lc = list_map (fun (prim, _) -> prim) g.Gto.lc
let lc = list_map (fun (prim, _) -> prim) g.Gto.lc
and lc' = list_map (fun (prim, _) -> prim) g'.Gto.lc
in
if lc <> lc' then find2 (s,g,n) a (i+1) else (a.(i) <- None ; i)
@ -313,13 +320,13 @@ end = struct
let ao_num = List.length long_basis |> AO_number.of_int in
let ao_prim_num =
list_map (fun (_,g,_) -> List.length g.Gto.lc
|> AO_prim_number.of_int ) long_basis
|> AO_prim_number.of_int ) long_basis
|> Array.of_list
and ao_nucl =
list_map (fun (_,_,n) -> n) long_basis
list_map (fun (_,_,n) -> n) long_basis
|> Array.of_list
and ao_power =
list_map (fun (x,_,_) -> x) long_basis
list_map (fun (x,_,_) -> x) long_basis
|> Array.of_list
in
let ao_prim_num_max = Array.fold_left (fun s x ->
@ -329,16 +336,16 @@ end = struct
in
let gtos =
list_map (fun (_,x,_) -> x) long_basis
list_map (fun (_,x,_) -> x) long_basis
in
let create_expo_coef ec =
let coefs =
begin match ec with
| `Coefs -> list_map (fun x->
list_map (fun (_,coef) -> AO_coef.to_float coef) x.Gto.lc ) gtos
list_map (fun (_,coef) -> AO_coef.to_float coef) x.Gto.lc ) gtos
| `Expos -> list_map (fun x->
list_map (fun (prim,_) -> AO_expo.to_float
prim.GaussianPrimitive.expo) x.Gto.lc ) gtos
prim.GaussianPrimitive.expo) x.Gto.lc ) gtos
end
in
let rec get_n n accu = function
@ -360,7 +367,7 @@ end = struct
let ao_coef = create_expo_coef `Coefs
|> Array.of_list
|> Array.map AO_coef.of_float
and ao_expo = create_expo_coef `Expos
and ao_expo = create_expo_coef `Expos
|> Array.of_list
|> Array.map AO_expo.of_float
in
@ -372,7 +379,7 @@ end = struct
}
;;
let reorder b =
let reorder b =
let order = ordering b in
let f a = Array.init (Array.length a) (fun i -> a.(order.(i))) in
let ao_prim_num_max = AO_prim_number.to_int b.ao_prim_num_max
@ -464,7 +471,7 @@ Basis set (read-only) ::
| line :: tail ->
let line = String.trim line in
if line = "Basis set (read-only) ::" then
String.concat "\n" tail
String.concat "\n" tail
else
extract_basis tail
in

5
ocaml/Input_mo_basis.ml
View File

@ -56,7 +56,10 @@ end = struct
let read_ao_md5 () =
let ao_md5 =
match (Input_ao_basis.Ao_basis.read ()) with
| None -> failwith "Unable to read AO basis"
| None -> ("None"
|> Digest.string
|> Digest.to_hex
|> MD5.of_string)
| Some result -> Input_ao_basis.Ao_basis.to_md5 result
in
let result =

146
scripts/qp_import_trexio.py
View File

@ -132,60 +132,113 @@ def write_ezfio(trexio_filename, filename):
try:
basis_type = trexio.read_basis_type(trexio_file)
if basis_type.lower() not in ["gaussian", "slater"]:
raise TypeError
if basis_type.lower() in ["gaussian", "slater"]:
shell_num = trexio.read_basis_shell_num(trexio_file)
prim_num = trexio.read_basis_prim_num(trexio_file)
ang_mom = trexio.read_basis_shell_ang_mom(trexio_file)
nucl_index = trexio.read_basis_nucleus_index(trexio_file)
exponent = trexio.read_basis_exponent(trexio_file)
coefficient = trexio.read_basis_coefficient(trexio_file)
shell_index = trexio.read_basis_shell_index(trexio_file)
ao_shell = trexio.read_ao_shell(trexio_file)
shell_num = trexio.read_basis_shell_num(trexio_file)
prim_num = trexio.read_basis_prim_num(trexio_file)
ang_mom = trexio.read_basis_shell_ang_mom(trexio_file)
nucl_index = trexio.read_basis_nucleus_index(trexio_file)
exponent = trexio.read_basis_exponent(trexio_file)
coefficient = trexio.read_basis_coefficient(trexio_file)
shell_index = trexio.read_basis_shell_index(trexio_file)
ao_shell = trexio.read_ao_shell(trexio_file)
ezfio.set_basis_basis("Read from TREXIO")
ezfio.set_ao_basis_ao_basis("Read from TREXIO")
ezfio.set_basis_shell_num(shell_num)
ezfio.set_basis_prim_num(prim_num)
ezfio.set_basis_shell_ang_mom(ang_mom)
ezfio.set_basis_basis_nucleus_index([ x+1 for x in nucl_index ])
ezfio.set_basis_prim_expo(exponent)
ezfio.set_basis_prim_coef(coefficient)
ezfio.set_basis_basis("Read from TREXIO")
ezfio.set_basis_shell_num(shell_num)
ezfio.set_basis_prim_num(prim_num)
ezfio.set_basis_shell_ang_mom(ang_mom)
ezfio.set_basis_basis_nucleus_index([ x+1 for x in nucl_index ])
ezfio.set_basis_prim_expo(exponent)
ezfio.set_basis_prim_coef(coefficient)
nucl_shell_num = []
prev = None
m = 0
for i in ao_shell:
if i != prev:
m += 1
if prev is None or nucl_index[i] != nucl_index[prev]:
nucl_shell_num.append(m)
m = 0
prev = i
assert (len(nucl_shell_num) == nucl_num)
nucl_shell_num = []
prev = None
m = 0
for i in ao_shell:
if i != prev:
m += 1
if prev is None or nucl_index[i] != nucl_index[prev]:
nucl_shell_num.append(m)
m = 0
prev = i
assert (len(nucl_shell_num) == nucl_num)
shell_prim_num = []
prev = shell_index[0]
count = 0
for i in shell_index:
if i != prev:
shell_prim_num.append(count)
count = 0
count += 1
prev = i
shell_prim_num.append(count)
shell_prim_num = []
prev = shell_index[0]
count = 0
for i in shell_index:
if i != prev:
shell_prim_num.append(count)
count = 0
count += 1
prev = i
shell_prim_num.append(count)
assert (len(shell_prim_num) == shell_num)
assert (len(shell_prim_num) == shell_num)
ezfio.set_basis_shell_prim_num(shell_prim_num)
ezfio.set_basis_shell_index([x+1 for x in shell_index])
ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
ezfio.set_basis_shell_prim_num(shell_prim_num)
ezfio.set_basis_shell_index([x+1 for x in shell_index])
ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
shell_factor = trexio.read_basis_shell_factor(trexio_file)
prim_factor = trexio.read_basis_prim_factor(trexio_file)
shell_factor = trexio.read_basis_shell_factor(trexio_file)
prim_factor = trexio.read_basis_prim_factor(trexio_file)
print("OK")
elif basis_type.lower() == "numerical":
shell_num = trexio.read_basis_shell_num(trexio_file)
prim_num = shell_num
ang_mom = trexio.read_basis_shell_ang_mom(trexio_file)
nucl_index = trexio.read_basis_nucleus_index(trexio_file)
exponent = [1.]*prim_num
coefficient = [1.]*prim_num
shell_index = [i for i in range(shell_num)]
ao_shell = trexio.read_ao_shell(trexio_file)
ezfio.set_basis_basis("None")
ezfio.set_ao_basis_ao_basis("None")
ezfio.set_basis_shell_num(shell_num)
ezfio.set_basis_prim_num(prim_num)
ezfio.set_basis_shell_ang_mom(ang_mom)
ezfio.set_basis_basis_nucleus_index([ x+1 for x in nucl_index ])
ezfio.set_basis_prim_expo(exponent)
ezfio.set_basis_prim_coef(coefficient)
nucl_shell_num = []
prev = None
m = 0
for i in ao_shell:
if i != prev:
m += 1
if prev is None or nucl_index[i] != nucl_index[prev]:
nucl_shell_num.append(m)
m = 0
prev = i
assert (len(nucl_shell_num) == nucl_num)
shell_prim_num = []
prev = shell_index[0]
count = 0
for i in shell_index:
if i != prev:
shell_prim_num.append(count)
count = 0
count += 1
prev = i
shell_prim_num.append(count)
assert (len(shell_prim_num) == shell_num)
ezfio.set_basis_shell_prim_num(shell_prim_num)
ezfio.set_basis_shell_index([x+1 for x in shell_index])
ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
shell_factor = trexio.read_basis_shell_factor(trexio_file)
prim_factor = [1.]*prim_num
else:
raise TypeError
print(basis_type)
except:
print("None")
ezfio.set_ao_basis_ao_cartesian(True)
@ -262,7 +315,6 @@ def write_ezfio(trexio_filename, filename):
# ezfio.set_ao_basis_ao_prim_num_max(prim_num_max)
ezfio.set_ao_basis_ao_coef(coef)
ezfio.set_ao_basis_ao_expo(expo)
ezfio.set_ao_basis_ao_basis("Read from TREXIO")
print("OK")

136
src/trexio/import_trexio_integrals.irp.f
View File

@ -3,6 +3,7 @@ program import_integrals_ao
implicit none
integer(trexio_t) :: f ! TREXIO file handle
integer(trexio_exit_code) :: rc
PROVIDE mo_num
f = trexio_open(trexio_filename, 'r', TREXIO_AUTO, rc)
if (f == 0_8) then
@ -42,10 +43,10 @@ subroutine run(f)
if (trexio_has_nucleus_repulsion(f) == TREXIO_SUCCESS) then
rc = trexio_read_nucleus_repulsion(f, s)
call trexio_assert(rc, TREXIO_SUCCESS)
if (rc /= TREXIO_SUCCESS) then
print *, irp_here, rc
print *, 'Error reading nuclear repulsion'
call trexio_assert(rc, TREXIO_SUCCESS)
stop -1
endif
call ezfio_set_nuclei_nuclear_repulsion(s)
@ -63,6 +64,7 @@ subroutine run(f)
if (rc /= TREXIO_SUCCESS) then
print *, irp_here
print *, 'Error reading AO overlap'
call trexio_assert(rc, TREXIO_SUCCESS)
stop -1
endif
call ezfio_set_ao_one_e_ints_ao_integrals_overlap(A)
@ -74,6 +76,7 @@ subroutine run(f)
if (rc /= TREXIO_SUCCESS) then
print *, irp_here
print *, 'Error reading AO kinetic integrals'
call trexio_assert(rc, TREXIO_SUCCESS)
stop -1
endif
call ezfio_set_ao_one_e_ints_ao_integrals_kinetic(A)
@ -85,6 +88,7 @@ subroutine run(f)
! if (rc /= TREXIO_SUCCESS) then
! print *, irp_here
! print *, 'Error reading AO ECP local integrals'
! call trexio_assert(rc, TREXIO_SUCCESS)
! stop -1
! endif
! call ezfio_set_ao_one_e_ints_ao_integrals_pseudo(A)
@ -96,6 +100,7 @@ subroutine run(f)
if (rc /= TREXIO_SUCCESS) then
print *, irp_here
print *, 'Error reading AO potential N-e integrals'
call trexio_assert(rc, TREXIO_SUCCESS)
stop -1
endif
call ezfio_set_ao_one_e_ints_ao_integrals_n_e(A)
@ -106,41 +111,112 @@ subroutine run(f)
! AO 2e integrals
! ---------------
PROVIDE ao_integrals_map
integer*4 :: BUFSIZE
BUFSIZE=ao_num**2
allocate(buffer_i(BUFSIZE), buffer_values(BUFSIZE))
allocate(Vi(4,BUFSIZE), V(BUFSIZE))
rc = trexio_has_ao_2e_int(f)
PROVIDE ao_num
if (rc /= TREXIO_HAS_NOT) then
PROVIDE ao_integrals_map
integer*8 :: offset, icount
integer*4 :: BUFSIZE
BUFSIZE=ao_num**2
allocate(buffer_i(BUFSIZE), buffer_values(BUFSIZE))
allocate(Vi(4,BUFSIZE), V(BUFSIZE))
offset = 0_8
icount = BUFSIZE
rc = TREXIO_SUCCESS
do while (icount == size(V))
rc = trexio_read_ao_2e_int_eri(f, offset, icount, Vi, V)
do m=1,icount
i = Vi(1,m)
j = Vi(2,m)
k = Vi(3,m)
l = Vi(4,m)
integral = V(m)
call two_e_integrals_index(i, j, k, l, buffer_i(m) )
buffer_values(m) = integral
enddo
call insert_into_ao_integrals_map(int(icount,4),buffer_i,buffer_values)
offset = offset + icount
integer*8 :: offset, icount
offset = 0_8
icount = BUFSIZE
rc = TREXIO_SUCCESS
do while (icount == size(V))
rc = trexio_read_ao_2e_int_eri(f, offset, icount, Vi, V)
do m=1,icount
i = Vi(1,m)
j = Vi(2,m)
k = Vi(3,m)
l = Vi(4,m)
integral = V(m)
call two_e_integrals_index(i, j, k, l, buffer_i(m) )
buffer_values(m) = integral
enddo
call insert_into_ao_integrals_map(int(icount,4),buffer_i,buffer_values)
offset = offset + icount
if (rc /= TREXIO_SUCCESS) then
exit
endif
end do
n_integrals = offset
call map_sort(ao_integrals_map)
call map_unique(ao_integrals_map)
call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map)
call ezfio_set_ao_two_e_ints_io_ao_two_e_integrals('Read')
deallocate(buffer_i, buffer_values, Vi, V)
print *, 'AO integrals read from TREXIO file'
else
print *, 'AO integrals not found in TREXIO file'
endif
! MO integrals
! ------------
allocate(A(mo_num, mo_num))
if (trexio_has_mo_1e_int_core_hamiltonian(f) == TREXIO_SUCCESS) then
rc = trexio_read_mo_1e_int_core_hamiltonian(f, A)
if (rc /= TREXIO_SUCCESS) then
exit
print *, irp_here
print *, 'Error reading MO 1e integrals'
call trexio_assert(rc, TREXIO_SUCCESS)
stop -1
endif
end do
n_integrals = offset
call ezfio_set_mo_one_e_ints_mo_one_e_integrals(A)
call ezfio_set_mo_one_e_ints_io_mo_one_e_integrals('Read')
endif
deallocate(A)
call map_sort(ao_integrals_map)
call map_unique(ao_integrals_map)
! MO 2e integrals
! ---------------
call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map)
call ezfio_set_ao_two_e_ints_io_ao_two_e_integrals('Read')
rc = trexio_has_mo_2e_int(f)
if (rc /= TREXIO_HAS_NOT) then
BUFSIZE=mo_num**2
allocate(buffer_i(BUFSIZE), buffer_values(BUFSIZE))
allocate(Vi(4,BUFSIZE), V(BUFSIZE))
offset = 0_8
icount = BUFSIZE
rc = TREXIO_SUCCESS
do while (icount == size(V))
rc = trexio_read_mo_2e_int_eri(f, offset, icount, Vi, V)
do m=1,icount
i = Vi(1,m)
j = Vi(2,m)
k = Vi(3,m)
l = Vi(4,m)
integral = V(m)
call two_e_integrals_index(i, j, k, l, buffer_i(m) )
buffer_values(m) = integral
enddo
call map_append(mo_integrals_map, buffer_i, buffer_values, int(icount,4))
offset = offset + icount
if (rc /= TREXIO_SUCCESS) then
exit
endif
end do
n_integrals = offset
call map_sort(mo_integrals_map)
call map_unique(mo_integrals_map)
call map_save_to_disk(trim(ezfio_filename)//'/work/mo_ints',mo_integrals_map)
call ezfio_set_mo_two_e_ints_io_mo_two_e_integrals('Read')
deallocate(buffer_i, buffer_values, Vi, V)
print *, 'MO integrals read from TREXIO file'
else
print *, 'MO integrals not found in TREXIO file'
endif
end