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mirror of https://github.com/QuantumPackage/qp2.git synced 2024-10-04 07:05:58 +02:00

Merge pull request #285 from AbdAmmar/dev-stable-tc-scf
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Dev stable tc scf
This commit is contained in:
AbdAmmar 2023-05-19 11:37:55 +02:00 committed by GitHub
commit 15dcd3d18f
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GPG Key ID: 4AEE18F83AFDEB23
169 changed files with 32611 additions and 1704 deletions

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@ -48,6 +48,7 @@ jobs:
./configure -i docopt || :
./configure -i resultsFile || :
./configure -i bats || :
./configure -i trexio-nohdf5 || :
./configure -c ./config/gfortran_debug.cfg
- name: Compilation
run: |

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@ -22,7 +22,7 @@ jobs:
- uses: actions/checkout@v3
- name: Install dependencies
run: |
sudo apt install gfortran gcc liblapack-dev libblas-dev wget python3 make m4 pkg-config
sudo apt install gfortran gcc liblapack-dev libblas-dev wget python3 make m4 pkg-config hdf5
- name: zlib
run: |
./configure -i zlib || echo OK
@ -50,6 +50,12 @@ jobs:
- name: bats
run: |
./configure -i bats || echo OK
- name: trexio-nohdf5
run: |
./configure -i trexio-nohdf5 || echo OK
- name: trexio
run: |
./configure -i trexio || echo OK
- name: Final check
run: |
./configure -c config/gfortran_debug.cfg

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@ -46,7 +46,7 @@ def main(arguments):
append_bats(dirname, filenames)
else:
for (dirname, _, filenames) in os.walk(os.getcwd(), followlinks=False):
if "IRPF90_temp" not in dirname:
if "IRPF90_temp" not in dirname and "external" not in dirname:
append_bats(dirname, filenames)
l_bats = [y for _, y in sorted(l_bats)]
@ -67,6 +67,7 @@ def main(arguments):
os.system(test+" python3 bats_to_sh.py "+bats_file+
"| bash")
else:
# print(" ".join(["bats", "--verbose-run", "--trace", bats_file]))
subprocess.check_call(["bats", "--verbose-run", "--trace", bats_file], env=os.environ)

37
configure vendored
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@ -9,6 +9,8 @@ echo "QP_ROOT="$QP_ROOT
unset CC
unset CCXX
TREXIO_VERSION=2.3.2
# Force GCC instead of ICC for dependencies
export CC=gcc
@ -189,7 +191,7 @@ if [[ "${PACKAGES}.x" != ".x" ]] ; then
fi
if [[ ${PACKAGES} = all ]] ; then
PACKAGES="zlib ninja zeromq f77zmq gmp ocaml docopt resultsFile bats"
PACKAGES="zlib ninja zeromq f77zmq gmp ocaml docopt resultsFile bats trexio"
fi
@ -203,6 +205,33 @@ for PACKAGE in ${PACKAGES} ; do
mv ninja "\${QP_ROOT}"/bin/
EOF
elif [[ ${PACKAGE} = trexio-nohdf5 ]] ; then
VERSION=$TREXIO_VERSION
execute << EOF
cd "\${QP_ROOT}"/external
wget https://github.com/TREX-CoE/trexio/releases/download/v${VERSION}/trexio-${VERSION}.tar.gz
tar -zxf trexio-${VERSION}.tar.gz
cd trexio-${VERSION}
./configure --prefix=\${QP_ROOT} --without-hdf5
make -j 8 && make -j 8 check && make -j 8 install
cp ${QP_ROOT}/include/trexio_f.f90 ${QP_ROOT}/src/ezfio_files
tar -zxvf "\${QP_ROOT}"/external/qp2-dependencies/${ARCHITECTURE}/ninja.tar.gz
mv ninja "\${QP_ROOT}"/bin/
EOF
elif [[ ${PACKAGE} = trexio ]] ; then
VERSION=$TREXIO_VERSION
execute << EOF
cd "\${QP_ROOT}"/external
wget https://github.com/TREX-CoE/trexio/releases/download/v${VERSION}/trexio-${VERSION}.tar.gz
tar -zxf trexio-${VERSION}.tar.gz
cd trexio-${VERSION}
./configure --prefix=\${QP_ROOT}
make -j 8 && make -j 8 check && make -j 8 install
cp ${QP_ROOT}/include/trexio_f.f90 ${QP_ROOT}/src/ezfio_files
EOF
elif [[ ${PACKAGE} = gmp ]] ; then
@ -338,6 +367,12 @@ if [[ ${ZEROMQ} = $(not_found) ]] ; then
fail
fi
TREXIO=$(find_lib -ltrexio)
if [[ ${TREXIO} = $(not_found) ]] ; then
error "TREXIO (trexio,trexio-nohdf5) is not installed. If you don't have HDF5, use trexio-nohdf5"
fail
fi
F77ZMQ=$(find_lib -lzmq -lf77zmq -lpthread)
if [[ ${F77ZMQ} = $(not_found) ]] ; then
error "Fortran binding of ZeroMQ (f77zmq) is not installed."

5
data/basis/none Normal file
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@ -0,0 +1,5 @@
$DATA
HYDROGEN
$END

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@ -110,6 +110,11 @@ function qp()
unset COMMAND
;;
"test")
shift
qp_test $@
;;
*)
which "qp_$1" &> /dev/null
if [[ $? -eq 0 ]] ; then
@ -183,7 +188,7 @@ _qp_Complete()
;;
esac;;
set_file)
COMPREPLY=( $(compgen -W "$(for i in * ; do [[ -f ${i}/ezfio/.version ]] && echo $i ; done)" -- ${cur} ) )
COMPREPLY=( $(compgen -W "$(for i in */ $(find . -name ezfio | sed 's/ezfio$/.version/') ; do [[ -f $i ]] && echo ${i%/.version} ; done)" -- ${cur} ) )
return 0
;;
plugins)
@ -215,10 +220,15 @@ _qp_Complete()
return 0
;;
esac;;
test)
COMPREPLY=( $(compgen -W "-v -a " -- $cur ) )
return 0
;;
*)
COMPREPLY=( $(compgen -W 'plugins set_file \
unset_file man \
create_ezfio \
test \
convert_output_to_ezfio \
-h update' -- $cur ) )

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@ -247,8 +247,7 @@ end = struct
let read () =
if (Ezfio.has_ao_basis_ao_basis ()) then
begin
try
let result =
{ ao_basis = read_ao_basis ();
ao_num = read_ao_num () ;
@ -267,9 +266,8 @@ end = struct
|> MD5.to_string
|> Ezfio.set_ao_basis_ao_md5 ;
Some result
end
else
None
with
| _ -> (Ezfio.set_ao_basis_ao_md5 "None" ; None)
;;

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@ -478,6 +478,7 @@ let run ?o b au c d m p cart xyz_file =
let nmax =
Nucl_number.get_max ()
in
let rec do_work (accu:(Atom.t*Nucl_number.t) list) (n:int) = function
| [] -> accu
| e::tail ->
@ -520,141 +521,144 @@ let run ?o b au c d m p cart xyz_file =
in
let long_basis = Long_basis.of_basis basis in
let ao_num = List.length long_basis in
Ezfio.set_ao_basis_ao_num ao_num;
Ezfio.set_ao_basis_ao_basis b;
Ezfio.set_basis_basis b;
let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
and ao_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
and ao_power=
let l = list_map (fun (x,_,_) -> x) long_basis in
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.x)) l)@
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.y)) l)@
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.z)) l)
in
let ao_prim_num_max = List.fold_left (fun s x ->
if x > s then x
else s) 0 ao_prim_num
in
let gtos =
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
| `Expos -> list_map (fun x->
list_map (fun (prim,_) -> AO_expo.to_float
prim.GaussianPrimitive.expo) x.Gto.lc) gtos
end
if ao_num > 0 then
begin
Ezfio.set_ao_basis_ao_num ao_num;
Ezfio.set_ao_basis_ao_basis b;
Ezfio.set_basis_basis b;
let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
and ao_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
and ao_power=
let l = list_map (fun (x,_,_) -> x) long_basis in
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.x)) l)@
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.y)) l)@
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.z)) l)
in
let rec get_n n accu = function
| [] -> List.rev accu
| h::tail ->
let y =
begin match List.nth_opt h n with
| Some x -> x
| None -> 0.
let ao_prim_num_max = List.fold_left (fun s x ->
if x > s then x
else s) 0 ao_prim_num
in
let gtos =
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
| `Expos -> list_map (fun x->
list_map (fun (prim,_) -> AO_expo.to_float
prim.GaussianPrimitive.expo) x.Gto.lc) gtos
end
in
get_n n (y::accu) tail
in
let rec get_n n accu = function
| [] -> List.rev accu
| h::tail ->
let y =
begin match List.nth_opt h n with
| Some x -> x
| None -> 0.
end
in
get_n n (y::accu) tail
in
let rec build accu = function
| n when n=ao_prim_num_max -> accu
| n -> build ( accu @ (get_n n [] coefs) ) (n+1)
in
build [] 0
in
let rec build accu = function
| n when n=ao_prim_num_max -> accu
| n -> build ( accu @ (get_n n [] coefs) ) (n+1)
in
build [] 0
in
let ao_coef = create_expo_coef `Coefs
and ao_expo = create_expo_coef `Expos
in
let () =
let shell_num = List.length basis in
let lc : (GaussianPrimitive.t * Qptypes.AO_coef.t) list list =
list_map ( fun (g,_) -> g.Gto.lc ) basis
in
let ang_mom =
list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) ->
let x, _ = List.hd l in
Angmom.to_l x.GaussianPrimitive.sym |> Qptypes.Positive_int.to_int
) lc
in
let expo =
list_map (fun l -> list_map (fun (x,_) -> Qptypes.AO_expo.to_float x.GaussianPrimitive.expo) l ) lc
|> List.concat
in
let coef =
list_map (fun l ->
list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l
) lc
|> List.concat
in
let shell_prim_num =
list_map List.length lc
in
let shell_idx =
let rec make_list n accu = function
| 0 -> accu
| i -> make_list n (n :: accu) (i-1)
let ao_coef = create_expo_coef `Coefs
and ao_expo = create_expo_coef `Expos
in
let rec aux count accu = function
| [] -> List.rev accu
| l::rest ->
let new_l = make_list count accu (List.length l) in
aux (count+1) new_l rest
in
aux 1 [] lc
in
let prim_num = List.length coef in
Ezfio.set_basis_typ "Gaussian";
Ezfio.set_basis_shell_num shell_num;
Ezfio.set_basis_prim_num prim_num ;
Ezfio.set_basis_shell_prim_num (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |]
~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis)
) ;
Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| nucl_num |]
~data:(
list_map (fun (_,n) -> Nucl_number.to_int n) basis
|> List.fold_left (fun accu i ->
match accu with
| [] -> [(1,i)]
| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((1,i)::(h,j)::rest)
) []
|> List.rev
|> List.map fst
)) ;
Ezfio.set_basis_prim_coef (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| prim_num |] ~data:coef) ;
Ezfio.set_basis_prim_expo (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| prim_num |] ~data:expo) ;
let () =
let shell_num = List.length basis in
let lc : (GaussianPrimitive.t * Qptypes.AO_coef.t) list list =
list_map ( fun (g,_) -> g.Gto.lc ) basis
in
let ang_mom =
list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) ->
let x, _ = List.hd l in
Angmom.to_l x.GaussianPrimitive.sym |> Qptypes.Positive_int.to_int
) lc
in
let expo =
list_map (fun l -> list_map (fun (x,_) -> Qptypes.AO_expo.to_float x.GaussianPrimitive.expo) l ) lc
|> List.concat
in
let coef =
list_map (fun l ->
list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l
) lc
|> List.concat
in
let shell_prim_num =
list_map List.length lc
in
let shell_idx =
let rec make_list n accu = function
| 0 -> accu
| i -> make_list n (n :: accu) (i-1)
in
let rec aux count accu = function
| [] -> List.rev accu
| l::rest ->
let new_l = make_list count accu (List.length l) in
aux (count+1) new_l rest
in
aux 1 [] lc
in
let prim_num = List.length coef in
Ezfio.set_basis_typ "Gaussian";
Ezfio.set_basis_shell_num shell_num;
Ezfio.set_basis_prim_num prim_num ;
Ezfio.set_basis_shell_prim_num (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |]
~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis)
) ;
Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| nucl_num |]
~data:(
list_map (fun (_,n) -> Nucl_number.to_int n) basis
|> List.fold_left (fun accu i ->
match accu with
| [] -> [(1,i)]
| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((1,i)::(h,j)::rest)
) []
|> List.rev
|> List.map fst
)) ;
Ezfio.set_basis_prim_coef (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| prim_num |] ~data:coef) ;
Ezfio.set_basis_prim_expo (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| prim_num |] ~data:expo) ;
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
Ezfio.set_ao_basis_ao_cartesian(cart);
in
match Input.Ao_basis.read () with
| None -> failwith "Error in basis"
| Some x -> Input.Ao_basis.write x
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
Ezfio.set_ao_basis_ao_cartesian(cart);
in
match Input.Ao_basis.read () with
| None -> failwith "Error in basis"
| Some x -> Input.Ao_basis.write x
end
in
let () =
try write_file () with
@ -781,7 +785,7 @@ If a file with the same name as the basis set exists, this file will be read. O
run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename
)
with
| Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt
(* | Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt *)
| Command_line.Error txt -> Printf.eprintf "Command line error: %s\n%!" txt

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@ -38,7 +38,7 @@ def comp_path(path):
from qp_path import QP_ROOT, QP_SRC, QP_EZFIO
LIB = " -lz"
LIB = " -lz -ltrexio"
EZFIO_LIB = join("$QP_ROOT", "lib", "libezfio_irp.a")
ZMQ_LIB = join("$QP_ROOT", "lib", "libf77zmq.a") + " " + join("$QP_ROOT", "lib", "libzmq.a") + " -lstdc++ -lrt -ldl"
ROOT_BUILD_NINJA = join("$QP_ROOT", "config", "build.ninja")

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@ -172,25 +172,23 @@ let run check_only ?ndet ?state ezfio_filename =
(* Reorder basis set *)
begin
let aos =
match Input.Ao_basis.read() with
| Some x -> x
| _ -> assert false
in
let ordering = Input.Ao_basis.ordering aos in
let test = Array.copy ordering in
Array.sort compare test ;
if test <> ordering then
begin
Printf.eprintf "Warning: Basis set is not properly ordered. Redordering.\n";
let new_aos = Input.Ao_basis.reorder aos in
Input.Ao_basis.write new_aos;
match Input.Mo_basis.read() with
| None -> ()
| Some mos ->
let new_mos = Input.Mo_basis.reorder mos ordering in
Input.Mo_basis.write new_mos
end
match Input.Ao_basis.read() with
| Some aos ->
let ordering = Input.Ao_basis.ordering aos in
let test = Array.copy ordering in
Array.sort compare test ;
if test <> ordering then
begin
Printf.eprintf "Warning: Basis set is not properly ordered. Redordering.\n";
let new_aos = Input.Ao_basis.reorder aos in
Input.Ao_basis.write new_aos;
match Input.Mo_basis.read() with
| None -> ()
| Some mos ->
let new_mos = Input.Mo_basis.reorder mos ordering in
Input.Mo_basis.write new_mos
end
| _ -> ()
end;
begin

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@ -42,13 +42,15 @@ import sys, os
import scipy
import scipy.stats
from math import sqrt, gamma, exp
import json
import qp_json
def read_data(filename,state):
def read_data(ezfio_filename,state):
""" Read energies and PT2 from input file """
with open(filename,'r') as f:
lines = json.load(f)['fci']
data = qp_json.load_last(ezfio_filename)
for method in data.keys():
x = data[method]
lines = x
print(f"State: {state}")
@ -138,15 +140,15 @@ def compute(data):
return mu, err, bias, p
filename = sys.argv[1]
print(filename)
ezfio_filename = sys.argv[1]
print(ezfio_filename)
if len(sys.argv) > 2:
state = int(sys.argv[2])
else:
state = 1
data = read_data(filename,state)
data = read_data(ezfio_filename,state)
mu, err, bias, _ = compute(data)
print(" %s: %8.3f +/- %5.3f eV\n"%(filename, mu, err))
print(" %s: %8.3f +/- %5.3f eV\n"%(ezfio_filename, mu, err))
import numpy as np
A = np.array( [ [ data[-1][1], 1. ],

View File

@ -1,57 +1,37 @@
#!/usr/bin/env python3
import re
import qp_json
import sys
# Read output file
with open(sys.argv[1], 'r') as file:
output = file.read()
if len(sys.argv) == 1:
print(f"syntax: {sys.argv[0]} EZFIO_FILE")
d = qp_json.load_all(sys.argv[1])
k = [ x for x in d.keys() ]
k.sort()
print("# Energy PT2 PT2_err rPT2 rPT2_err exFCI\n")
for f in k:
try:
j = d[f]["fci"]
except:
continue
print(f"# {f}")
for e in j:
out = f" {e['n_det']:8d}"
nstates = len(e["states"])
for ee in e["states"]:
try:
exc_energy = ee['ex_energy'][0]
except:
exc_energy = 0.
out += f" {ee['energy']:16.8f} {ee['pt2']:e} {ee['pt2_err']:e} {ee['rpt2']:e} {ee['rpt2_err']:e} {exc_energy:16.8f}"
print(out)
print("\n")
def extract_data(output):
lines = output.split("\n")
data = []
n_det = None
e = None
pt2 = None
err_pt2 = None
rpt2 = None
err_rpt2 = None
e_ex = None
reading = False
for iline, line in enumerate(lines):
if line.startswith("Summary at N_det"):
reading = False
if not reading and line.startswith(" N_det "):
n_det = int(re.search(r"N_det\s+=\s+(\d+)", line).group(1))
reading = True
if reading:
if line.startswith(" E "):
e = float(re.search(r"E\s+=\s+(-?\d+\.\d+)", line).group(1))
elif line.startswith(" PT2 "):
pt2 = float(re.search(r"PT2\s+=\s+(-?\d+\.\d+E?.\d*)", line).group(1))
err_pt2 = float(re.search(r"\+/-\s+(-?\d+\.\d+E?.\d*)", line).group(1))
elif line.startswith(" rPT2 "):
rpt2 = float(re.search(r"rPT2\s+=\s+(-?\d+\.\d+E?.\d*)", line).group(1))
err_rpt2 = float(re.search(r"\+/-\s+(-?\d+\.\d+E?.\d*)", line).group(1))
elif "minimum PT2 Extrapolated energy" in line:
e_ex_line = lines[iline+2]
e_ex = float(e_ex_line.split()[1])
reading = False
new_data = " {:8d} {:16.8f} {:e} {:e} {:e} {:e} {:16.8f}".format(n_det, e, pt2, err_pt2, rpt2, err_rpt2, e_ex)
data.append(new_data)
n_det = e = pt2 = err_pt2 = rpt2 = err_rpt2 = e_ex = None
return data
data = extract_data(output)
for item in data:
print(item)

View File

@ -0,0 +1,66 @@
#!/usr/bin/env python
import os
import json
def fix_json(s):
"""Properly termitates an incomplete JSON file"""
s = s.replace(' ','')
s = s.replace('\n','')
s = s.replace('\t','')
s = s.replace(",{}",'')
tmp = [ c for c in s if c in "[]{}" ]
tmp = "".join(tmp)
tmp_old = ""
while tmp != tmp_old:
tmp_old = tmp
tmp = tmp.replace("{}","")
tmp = tmp.replace("[]","")
while s[-1] in [ ',', '\n', ' ', '\t' ]:
s = s[:-1]
tmp = [ c for c in tmp ]
tmp.reverse()
for c in tmp:
if c == '[': s += "]"
elif c == '{': s += "}"
return s
def load(filename):
"""Loads a JSON file after calling the fix_json function."""
with open(filename,'r') as f:
data = f.read()
new_data = fix_json(data)
return json.loads(new_data)
def load_all(ezfio_filename):
"""Loads all JSON files of an EZFIO."""
d = {}
prefix = ezfio_filename+'/json/'
for filename in [ x for x in os.listdir(prefix) if x.endswith(".json")]:
d[filename] = load(prefix+filename)
return d
def load_last(ezfio_filename):
"""Loads last JSON file of an EZFIO."""
d = {}
prefix = ezfio_filename+'/json/'
l = [ x for x in os.listdir(prefix) if x.endswith(".json")]
l.sort()
filename = l[-1]
print(filename)
return load(prefix+filename)
def fix(ezfio_filename):
"""Fixes all JSON files in an EZFIO."""
d = load_all(ezfio_filename)
prefix = ezfio_filename+'/json/'
for filename in d.keys():
with open(prefix+filename, 'w') as json_file:
json.dump(d[filename], json_file)

View File

@ -12,21 +12,21 @@ double precision function ao_value(i,r)
integer :: power_ao(3)
double precision :: accu,dx,dy,dz,r2
num_ao = ao_nucl(i)
! power_ao(1:3)= ao_power(i,1:3)
! center_ao(1:3) = nucl_coord(num_ao,1:3)
! dx = (r(1) - center_ao(1))
! dy = (r(2) - center_ao(2))
! dz = (r(3) - center_ao(3))
! r2 = dx*dx + dy*dy + dz*dz
! dx = dx**power_ao(1)
! dy = dy**power_ao(2)
! dz = dz**power_ao(3)
power_ao(1:3)= ao_power(i,1:3)
center_ao(1:3) = nucl_coord(num_ao,1:3)
dx = (r(1) - center_ao(1))
dy = (r(2) - center_ao(2))
dz = (r(3) - center_ao(3))
r2 = dx*dx + dy*dy + dz*dz
dx = dx**power_ao(1)
dy = dy**power_ao(2)
dz = dz**power_ao(3)
accu = 0.d0
! do m=1,ao_prim_num(i)
! beta = ao_expo_ordered_transp(m,i)
! accu += ao_coef_normalized_ordered_transp(m,i) * dexp(-beta*r2)
! enddo
do m=1,ao_prim_num(i)
beta = ao_expo_ordered_transp(m,i)
accu += ao_coef_normalized_ordered_transp(m,i) * dexp(-beta*r2)
enddo
ao_value = accu * dx * dy * dz
end

View File

@ -7,17 +7,17 @@ BEGIN_PROVIDER [integer, List_all_comb_b2_size]
PROVIDE j1b_type
if(j1b_type .eq. 3) then
if((j1b_type .eq. 3) .or. (j1b_type .eq. 103)) then
List_all_comb_b2_size = 2**nucl_num
elseif(j1b_type .eq. 4) then
elseif((j1b_type .eq. 4) .or. (j1b_type .eq. 104)) then
List_all_comb_b2_size = nucl_num + 1
else
print *, 'j1b_type = ', j1b_pen, 'is not implemented'
print *, 'j1b_type = ', j1b_type, 'is not implemented'
stop
endif
@ -67,7 +67,7 @@ END_PROVIDER
List_all_comb_b2_expo = 0.d0
List_all_comb_b2_cent = 0.d0
if(j1b_type .eq. 3) then
if((j1b_type .eq. 3) .or. (j1b_type .eq. 103)) then
do i = 1, List_all_comb_b2_size
@ -121,7 +121,7 @@ END_PROVIDER
List_all_comb_b2_coef(i) = (-1.d0)**dble(phase) * dexp(-List_all_comb_b2_coef(i))
enddo
elseif(j1b_type .eq. 4) then
elseif((j1b_type .eq. 4) .or. (j1b_type .eq. 104)) then
List_all_comb_b2_coef( 1) = 1.d0
List_all_comb_b2_expo( 1) = 0.d0
@ -136,7 +136,7 @@ END_PROVIDER
else
print *, 'j1b_type = ', j1b_pen, 'is not implemented'
print *, 'j1b_type = ', j1b_type, 'is not implemented'
stop
endif
@ -156,18 +156,18 @@ BEGIN_PROVIDER [ integer, List_all_comb_b3_size]
implicit none
double precision :: tmp
if(j1b_type .eq. 3) then
if((j1b_type .eq. 3) .or. (j1b_type .eq. 103)) then
List_all_comb_b3_size = 3**nucl_num
elseif(j1b_type .eq. 4) then
elseif((j1b_type .eq. 4) .or. (j1b_type .eq. 104)) then
tmp = 0.5d0 * dble(nucl_num) * (dble(nucl_num) + 3.d0)
List_all_comb_b3_size = int(tmp) + 1
else
print *, 'j1b_type = ', j1b_pen, 'is not implemented'
print *, 'j1b_type = ', j1b_type, 'is not implemented'
stop
endif
@ -230,7 +230,7 @@ END_PROVIDER
List_all_comb_b3_expo = 0.d0
List_all_comb_b3_cent = 0.d0
if(j1b_type .eq. 3) then
if((j1b_type .eq. 3) .or. (j1b_type .eq. 103)) then
do i = 1, List_all_comb_b3_size
@ -287,7 +287,7 @@ END_PROVIDER
List_all_comb_b3_coef(i) = (-1.d0)**dble(phase) * facto * dexp(-List_all_comb_b3_coef(i))
enddo
elseif(j1b_type .eq. 4) then
elseif((j1b_type .eq. 4) .or. (j1b_type .eq. 104)) then
ii = 1
List_all_comb_b3_coef( ii) = 1.d0
@ -347,7 +347,7 @@ END_PROVIDER
else
print *, 'j1b_type = ', j1b_pen, 'is not implemented'
print *, 'j1b_type = ', j1b_type, 'is not implemented'
stop
endif

View File

@ -1,2 +1,3 @@
ao_basis
pseudo
cosgtos_ao_int

View File

@ -1,75 +1,99 @@
BEGIN_PROVIDER [ double precision, ao_overlap,(ao_num,ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_overlap_x,(ao_num,ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_overlap_y,(ao_num,ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_overlap_z,(ao_num,ao_num) ]
implicit none
! ---
BEGIN_PROVIDER [ double precision, ao_overlap , (ao_num, ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_overlap_x, (ao_num, ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_overlap_y, (ao_num, ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_overlap_z, (ao_num, ao_num) ]
BEGIN_DOC
! Overlap between atomic basis functions:
!
! :math:`\int \chi_i(r) \chi_j(r) dr`
! Overlap between atomic basis functions:
!
! :math:`\int \chi_i(r) \chi_j(r) dr`
END_DOC
integer :: i,j,n,l
double precision :: f
integer :: dim1
implicit none
integer :: i, j, n, l, dim1, power_A(3), power_B(3)
double precision :: overlap, overlap_x, overlap_y, overlap_z
double precision :: alpha, beta, c
double precision :: A_center(3), B_center(3)
integer :: power_A(3), power_B(3)
ao_overlap = 0.d0
ao_overlap = 0.d0
ao_overlap_x = 0.d0
ao_overlap_y = 0.d0
ao_overlap_z = 0.d0
if (read_ao_integrals_overlap) then
call ezfio_get_ao_one_e_ints_ao_integrals_overlap(ao_overlap(1:ao_num, 1:ao_num))
print *, 'AO overlap integrals read from disk'
if(read_ao_integrals_overlap) then
call ezfio_get_ao_one_e_ints_ao_integrals_overlap(ao_overlap(1:ao_num, 1:ao_num))
print *, 'AO overlap integrals read from disk'
else
dim1=100
!$OMP PARALLEL DO SCHEDULE(GUIDED) &
!$OMP DEFAULT(NONE) &
!$OMP PRIVATE(A_center,B_center,power_A,power_B,&
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
!$OMP alpha, beta,i,j,c) &
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
!$OMP ao_overlap_x,ao_overlap_y,ao_overlap_z,ao_overlap,ao_num,ao_coef_normalized_ordered_transp,ao_nucl, &
!$OMP ao_expo_ordered_transp,dim1)
do j=1,ao_num
A_center(1) = nucl_coord( ao_nucl(j), 1 )
A_center(2) = nucl_coord( ao_nucl(j), 2 )
A_center(3) = nucl_coord( ao_nucl(j), 3 )
power_A(1) = ao_power( j, 1 )
power_A(2) = ao_power( j, 2 )
power_A(3) = ao_power( j, 3 )
do i= 1,ao_num
B_center(1) = nucl_coord( ao_nucl(i), 1 )
B_center(2) = nucl_coord( ao_nucl(i), 2 )
B_center(3) = nucl_coord( ao_nucl(i), 3 )
power_B(1) = ao_power( i, 1 )
power_B(2) = ao_power( i, 2 )
power_B(3) = ao_power( i, 3 )
do n = 1,ao_prim_num(j)
alpha = ao_expo_ordered_transp(n,j)
do l = 1, ao_prim_num(i)
beta = ao_expo_ordered_transp(l,i)
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,overlap_y,overlap_z,overlap,dim1)
c = ao_coef_normalized_ordered_transp(n,j) * ao_coef_normalized_ordered_transp(l,i)
ao_overlap(i,j) += c * overlap
if(isnan(ao_overlap(i,j)))then
print*,'i,j',i,j
print*,'l,n',l,n
print*,'c,overlap',c,overlap
print*,overlap_x,overlap_y,overlap_z
stop
endif
ao_overlap_x(i,j) += c * overlap_x
ao_overlap_y(i,j) += c * overlap_y
ao_overlap_z(i,j) += c * overlap_z
if(use_cosgtos) then
!print*, ' use_cosgtos for ao_overlap ?', use_cosgtos
do j = 1, ao_num
do i = 1, ao_num
ao_overlap (i,j) = ao_overlap_cosgtos (i,j)
ao_overlap_x(i,j) = ao_overlap_cosgtos_x(i,j)
ao_overlap_y(i,j) = ao_overlap_cosgtos_y(i,j)
ao_overlap_z(i,j) = ao_overlap_cosgtos_z(i,j)
enddo
enddo
else
dim1=100
!$OMP PARALLEL DO SCHEDULE(GUIDED) &
!$OMP DEFAULT(NONE) &
!$OMP PRIVATE(A_center,B_center,power_A,power_B,&
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
!$OMP alpha, beta,i,j,c) &
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
!$OMP ao_overlap_x,ao_overlap_y,ao_overlap_z,ao_overlap,ao_num,ao_coef_normalized_ordered_transp,ao_nucl, &
!$OMP ao_expo_ordered_transp,dim1)
do j=1,ao_num
A_center(1) = nucl_coord( ao_nucl(j), 1 )
A_center(2) = nucl_coord( ao_nucl(j), 2 )
A_center(3) = nucl_coord( ao_nucl(j), 3 )
power_A(1) = ao_power( j, 1 )
power_A(2) = ao_power( j, 2 )
power_A(3) = ao_power( j, 3 )
do i= 1,ao_num
B_center(1) = nucl_coord( ao_nucl(i), 1 )
B_center(2) = nucl_coord( ao_nucl(i), 2 )
B_center(3) = nucl_coord( ao_nucl(i), 3 )
power_B(1) = ao_power( i, 1 )
power_B(2) = ao_power( i, 2 )
power_B(3) = ao_power( i, 3 )
do n = 1,ao_prim_num(j)
alpha = ao_expo_ordered_transp(n,j)
do l = 1, ao_prim_num(i)
beta = ao_expo_ordered_transp(l,i)
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,overlap_y,overlap_z,overlap,dim1)
c = ao_coef_normalized_ordered_transp(n,j) * ao_coef_normalized_ordered_transp(l,i)
ao_overlap(i,j) += c * overlap
if(isnan(ao_overlap(i,j)))then
print*,'i,j',i,j
print*,'l,n',l,n
print*,'c,overlap',c,overlap
print*,overlap_x,overlap_y,overlap_z
stop
endif
ao_overlap_x(i,j) += c * overlap_x
ao_overlap_y(i,j) += c * overlap_y
ao_overlap_z(i,j) += c * overlap_z
enddo
enddo
enddo
enddo
enddo
enddo
!$OMP END PARALLEL DO
!$OMP END PARALLEL DO
endif
endif
if (write_ao_integrals_overlap) then
call ezfio_set_ao_one_e_ints_ao_integrals_overlap(ao_overlap(1:ao_num, 1:ao_num))
print *, 'AO overlap integrals written to disk'
@ -77,6 +101,8 @@
END_PROVIDER
! ---
BEGIN_PROVIDER [ double precision, ao_overlap_imag, (ao_num, ao_num) ]
implicit none
BEGIN_DOC
@ -85,6 +111,8 @@ BEGIN_PROVIDER [ double precision, ao_overlap_imag, (ao_num, ao_num) ]
ao_overlap_imag = 0.d0
END_PROVIDER
! ---
BEGIN_PROVIDER [ complex*16, ao_overlap_complex, (ao_num, ao_num) ]
implicit none
BEGIN_DOC
@ -98,41 +126,43 @@ BEGIN_PROVIDER [ complex*16, ao_overlap_complex, (ao_num, ao_num) ]
enddo
END_PROVIDER
! ---
BEGIN_PROVIDER [ double precision, ao_overlap_abs, (ao_num, ao_num) ]
BEGIN_PROVIDER [ double precision, ao_overlap_abs,(ao_num,ao_num) ]
implicit none
BEGIN_DOC
! Overlap between absolute values of atomic basis functions:
!
! :math:`\int |\chi_i(r)| |\chi_j(r)| dr`
! Overlap between absolute values of atomic basis functions:
!
! :math:`\int |\chi_i(r)| |\chi_j(r)| dr`
END_DOC
integer :: i,j,n,l
double precision :: f
integer :: dim1
double precision :: overlap, overlap_x, overlap_y, overlap_z
implicit none
integer :: i, j, n, l, dim1, power_A(3), power_B(3)
double precision :: overlap_x, overlap_y, overlap_z
double precision :: alpha, beta
double precision :: A_center(3), B_center(3)
integer :: power_A(3), power_B(3)
double precision :: lower_exp_val, dx
if (is_periodic) then
do j=1,ao_num
do i= 1,ao_num
ao_overlap_abs(i,j)= cdabs(ao_overlap_complex(i,j))
if(is_periodic) then
do j = 1, ao_num
do i = 1, ao_num
ao_overlap_abs(i,j) = cdabs(ao_overlap_complex(i,j))
enddo
enddo
else
dim1=100
lower_exp_val = 40.d0
!$OMP PARALLEL DO SCHEDULE(GUIDED) &
!$OMP DEFAULT(NONE) &
!$OMP PRIVATE(A_center,B_center,power_A,power_B, &
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
!$OMP alpha, beta,i,j,dx) &
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
!$OMP ao_overlap_abs,ao_num,ao_coef_normalized_ordered_transp,ao_nucl,&
!$OMP ao_expo_ordered_transp,dim1,lower_exp_val)
!$OMP PARALLEL DO SCHEDULE(GUIDED) &
!$OMP DEFAULT(NONE) &
!$OMP PRIVATE(A_center,B_center,power_A,power_B, &
!$OMP overlap_x,overlap_y, overlap_z, &
!$OMP alpha, beta,i,j,dx) &
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
!$OMP ao_overlap_abs,ao_num,ao_coef_normalized_ordered_transp,ao_nucl,&
!$OMP ao_expo_ordered_transp,dim1,lower_exp_val)
do j=1,ao_num
A_center(1) = nucl_coord( ao_nucl(j), 1 )
A_center(2) = nucl_coord( ao_nucl(j), 2 )
@ -160,10 +190,14 @@ BEGIN_PROVIDER [ double precision, ao_overlap_abs,(ao_num,ao_num) ]
enddo
enddo
enddo
!$OMP END PARALLEL DO
!$OMP END PARALLEL DO
endif
END_PROVIDER
! ---
BEGIN_PROVIDER [ double precision, S_inv,(ao_num,ao_num) ]
implicit none
BEGIN_DOC

View File

@ -1,7 +1,10 @@
BEGIN_PROVIDER [ double precision, ao_deriv2_x,(ao_num,ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_deriv2_y,(ao_num,ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_deriv2_z,(ao_num,ao_num) ]
implicit none
! ---
BEGIN_PROVIDER [ double precision, ao_deriv2_x, (ao_num, ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_deriv2_y, (ao_num, ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_deriv2_z, (ao_num, ao_num) ]
BEGIN_DOC
! Second derivative matrix elements in the |AO| basis.
!
@ -11,114 +14,131 @@
! \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
!
END_DOC
integer :: i,j,n,l
double precision :: f
integer :: dim1
implicit none
integer :: i, j, n, l, dim1, power_A(3), power_B(3)
double precision :: overlap, overlap_y, overlap_z
double precision :: overlap_x0, overlap_y0, overlap_z0
double precision :: alpha, beta, c
double precision :: A_center(3), B_center(3)
integer :: power_A(3), power_B(3)
double precision :: d_a_2,d_2
dim1=100
! -- Dummy call to provide everything
A_center(:) = 0.d0
B_center(:) = 1.d0
alpha = 1.d0
beta = .1d0
power_A = 1
power_B = 0
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,overlap_y,d_a_2,overlap_z,overlap,dim1)
! --
if(use_cosgtos) then
!print*, 'use_cosgtos for ao_kinetic_integrals ?', use_cosgtos
!$OMP PARALLEL DO SCHEDULE(GUIDED) &
!$OMP DEFAULT(NONE) &
!$OMP PRIVATE(A_center,B_center,power_A,power_B,&
!$OMP overlap_y, overlap_z, overlap, &
!$OMP alpha, beta,i,j,c,d_a_2,d_2,deriv_tmp, &
!$OMP overlap_x0,overlap_y0,overlap_z0) &
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
!$OMP ao_deriv2_x,ao_deriv2_y,ao_deriv2_z,ao_num,ao_coef_normalized_ordered_transp,ao_nucl, &
!$OMP ao_expo_ordered_transp,dim1)
do j=1,ao_num
A_center(1) = nucl_coord( ao_nucl(j), 1 )
A_center(2) = nucl_coord( ao_nucl(j), 2 )
A_center(3) = nucl_coord( ao_nucl(j), 3 )
power_A(1) = ao_power( j, 1 )
power_A(2) = ao_power( j, 2 )
power_A(3) = ao_power( j, 3 )
do i= 1,ao_num
ao_deriv2_x(i,j)= 0.d0
ao_deriv2_y(i,j)= 0.d0
ao_deriv2_z(i,j)= 0.d0
B_center(1) = nucl_coord( ao_nucl(i), 1 )
B_center(2) = nucl_coord( ao_nucl(i), 2 )
B_center(3) = nucl_coord( ao_nucl(i), 3 )
power_B(1) = ao_power( i, 1 )
power_B(2) = ao_power( i, 2 )
power_B(3) = ao_power( i, 3 )
do n = 1,ao_prim_num(j)
alpha = ao_expo_ordered_transp(n,j)
do l = 1, ao_prim_num(i)
beta = ao_expo_ordered_transp(l,i)
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,overlap_x0,overlap_y0,overlap_z0,overlap,dim1)
c = ao_coef_normalized_ordered_transp(n,j) * ao_coef_normalized_ordered_transp(l,i)
do j = 1, ao_num
do i = 1, ao_num
ao_deriv2_x(i,j) = ao_deriv2_cosgtos_x(i,j)
ao_deriv2_y(i,j) = ao_deriv2_cosgtos_y(i,j)
ao_deriv2_z(i,j) = ao_deriv2_cosgtos_z(i,j)
enddo
enddo
power_A(1) = power_A(1)-2
if (power_A(1)>-1) then
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,d_a_2,overlap_y,overlap_z,overlap,dim1)
else
d_a_2 = 0.d0
endif
power_A(1) = power_A(1)+4
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,d_2,overlap_y,overlap_z,overlap,dim1)
power_A(1) = power_A(1)-2
else
double precision :: deriv_tmp
deriv_tmp = (-2.d0 * alpha * (2.d0 * power_A(1) +1.d0) * overlap_x0 &
+power_A(1) * (power_A(1)-1.d0) * d_a_2 &
+4.d0 * alpha * alpha * d_2 )*overlap_y0*overlap_z0