LCPQ/quantum_package
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Merge pull request #213 from scemama/master

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Bug fixes and OCaml  4.04
This commit is contained in:
Thomas Applencourt 2017-09-20 09:59:11 -05:00 committed by GitHub
commit b4f518f44d
137 changed files with 1371 additions and 985 deletions
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10
.travis.yml
View File

@ -4,19 +4,22 @@
# - sudo apt-get install gfortran liblapack-dev gcc
# - sudo apt-get install graphviz
os: linux
dist: trusty
sudo: false
compiler: gfortran
addons:
apt:
packages:
- gfortran
- gcc
- liblapack-dev
# - liblapack-dev
# - libblas-dev
- graphviz
# - zlib1g-dev
# - libgmp3-dev
cache:
directories:
@ -29,6 +32,7 @@ python:
script:
- ./configure ./config/travis.cfg
- source ./quantum_package.rc ; qp_module.py install Full_CI Full_CI_ZMQ Hartree_Fock CAS_SD_ZMQ mrcepa0 All_singles
- source ./quantum_package.rc ; cd ~ ; install_lapack.sh ; cd $QP_ROOT
- source ./quantum_package.rc ; ninja
- source ./quantum_package.rc ; cd ocaml ; make ; cd -
- source ./quantum_package.rc ; cd tests ; ./run_tests.sh -v

7
README.md
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@ -1,3 +1,10 @@
## IMPORTANT
If you have problems upgrading to the current version, consider re-installing everything from scratch including the OCaml compiler.
To do this, you will have to remove the `quantum_package` directory **and** the `$HOME/.opam` directory as well.
![QP](https://raw.githubusercontent.com/LCPQ/quantum_package/master/data/qp.png)
[![Build Status](https://travis-ci.org/LCPQ/quantum_package.svg?branch=master)](https://travis-ci.org/LCPQ/quantum_package)
[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/LCPQ/quantum_package?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

6
bin/qp_gaspi_run Executable file
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@ -0,0 +1,6 @@
#!/bin/bash
QP_ROOT=$( cd $(dirname "${BASH_SOURCE}")/.. ; pwd -P )
source $HOME/.bashrc
source $QP_ROOT/quantum_package.rc
exec $QP_ROOT/ocaml/qp_run $@

2
config/gfortran.cfg
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@ -11,7 +11,7 @@
#
[COMMON]
FC : gfortran -ffree-line-length-none -I .
LAPACK_LIB : -llapack -lblas
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32

2
config/gfortran_debug.cfg
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@ -11,7 +11,7 @@
#
[COMMON]
FC : gfortran -g -ffree-line-length-none -I .
LAPACK_LIB : -llapack -lblas
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert

2
config/travis.cfg
View File

@ -11,7 +11,7 @@
#
[COMMON]
FC : gfortran -ffree-line-length-none -I . -g
LAPACK_LIB : -llapack -lblas
LAPACK_LIB : -llapack -lrefblas -ltmglib
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert

13
configure vendored
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@ -43,6 +43,7 @@ except KeyError:
QP_ROOT_BIN = join(QP_ROOT, "bin")
QP_ROOT_LIB = join(QP_ROOT, "lib")
QP_ROOT_LIB64 = join(QP_ROOT, "lib64")
QP_ROOT_INSTALL = join(QP_ROOT, "install")
os.environ["PATH"] = os.environ["PATH"] + ":" + QP_ROOT_BIN
@ -65,6 +66,7 @@ d_dependency = {
"python": [],
"ninja": ["g++", "python"],
"make": [],
"gpi2": ["g++", "make"],
"p_graphviz": ["python"],
"bats": []
}
@ -140,6 +142,11 @@ f77zmq = Info(
description=' F77-ZeroMQ',
default_path=join(QP_ROOT_LIB, "libf77zmq.a") )
gpi2 = Info(
url='https://github.com/cc-hpc-itwm/GPI-2/archive/v1.3.0.tar.gz',
description=' GPI-2',
default_path=join(QP_ROOT_LIB64, "libGPI2.a") )
p_graphviz = Info(
url='https://github.com/xflr6/graphviz/archive/master.tar.gz',
description=' Python library for graphviz',
@ -154,7 +161,7 @@ d_info = dict()
for m in ["ocaml", "m4", "curl", "zlib", "patch", "irpf90", "docopt",
"resultsFile", "ninja", "emsl", "ezfio", "p_graphviz",
"zeromq", "f77zmq","bats"]:
"zeromq", "f77zmq", "bats", "gpi2"]:
exec ("d_info['{0}']={0}".format(m))
@ -481,8 +488,8 @@ def create_ninja_and_rc(l_installed):
'export NINJA={0}'.format(path_ninja.replace(QP_ROOT,"${QP_ROOT}")),
'export PYTHONPATH="${QP_EZFIO}/Python":"${QP_PYTHON}":"${PYTHONPATH}"',
'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"',
'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"',
'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"',
'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${QP_ROOT}"/lib64:"${LD_LIBRARY_PATH}"',
'export LIBRARY_PATH="${QP_ROOT}"/lib:"${QP_ROOT}"/lib64:"${LIBRARY_PATH}"',
'export C_INCLUDE_PATH="${C_INCLUDE_PATH}":"${QP_ROOT}"/include',
'',
'source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh',

15
install/scripts/install_gpi2.sh Executable file
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@ -0,0 +1,15 @@
#!/bin/bash -x
TARGET=gpi2
#GPI_OPTIONS=--with-infiniband
GPI_OPTIONS=--with-ethernet
function _install()
{
cd gpi2
./install.sh -p $QP_ROOT $GPI_OPTIONS
cp src/GASPI.f90 $QP_ROOT/src/plugins/GPI2/
return 0
}
source scripts/build.sh

10
install/scripts/install_lapack.sh Executable file
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@ -0,0 +1,10 @@
#!/bin/bash -x
git clone https://github.com/Reference-LAPACK/lapack-release.git
cd lapack-release
cp make.inc.example make.inc
make -j 8
mv librefblas.a liblapack.a libtmglib.a $QP_ROOT/lib

6
install/scripts/install_ocaml.sh
View File

@ -5,8 +5,7 @@ QP_ROOT=$PWD
cd -
# Normal installation
PACKAGES="core cryptokit.1.10 ocamlfind sexplib ZMQ"
#ppx_sexp_conv
PACKAGES="core cryptokit.1.10 ocamlfind sexplib ZMQ ppx_sexp_conv ppx_deriving"
# Needed for ZeroMQ
export C_INCLUDE_PATH="${QP_ROOT}"/include:"${C_INCLUDE_PATH}"
@ -64,7 +63,7 @@ fi
cd Downloads || exit 1
chmod +x ocaml.sh || exit 1
echo N | ./ocaml.sh ${QP_ROOT}/bin/ 4.02.1 || exit 1
echo N | ./ocaml.sh ${QP_ROOT}/bin/ 4.04.2 || exit 1
${QP_ROOT}/bin/opam config setup -a -q || exit 1
@ -76,7 +75,6 @@ source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true
NCPUs=$(cat /proc/cpuinfo | grep -i MHz | wc -l)
${QP_ROOT}/bin/opam install -j ${NCPUs} stdint.0.4.2 -y -q || exit 1
${QP_ROOT}/bin/opam install -j ${NCPUs} ZMQ -y -q || exit 1
${QP_ROOT}/bin/opam install -j ${NCPUs} ${PACKAGES} -y -q || exit 1
rm -f ../_build/ocaml.log

7
ocaml/Address.ml
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@ -1,4 +1,3 @@
open Core.Std
module Tcp : sig
type t
@ -8,7 +7,7 @@ module Tcp : sig
end = struct
type t = string
let of_string x =
if not (String.is_prefix ~prefix:"tcp://" x) then
if not (String_ext.is_prefix ~prefix:"tcp://" x) then
invalid_arg "Address Invalid"
;
x
@ -26,7 +25,7 @@ module Ipc : sig
end = struct
type t = string
let of_string x =
assert (String.is_prefix ~prefix:"ipc://" x);
assert (String_ext.is_prefix ~prefix:"ipc://" x);
x
let create name =
Printf.sprintf "ipc://%s" name
@ -41,7 +40,7 @@ module Inproc : sig
end = struct
type t = string
let of_string x =
assert (String.is_prefix ~prefix:"inproc://" x);
assert (String_ext.is_prefix ~prefix:"inproc://" x);
x
let create name =
Printf.sprintf "inproc://%s" name

4
ocaml/Atom.ml
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@ -1,4 +1,4 @@
open Core.Std
open Core
exception AtomError of string
@ -6,7 +6,7 @@ type t =
{ element : Element.t ;
charge : Charge.t ;
coord : Point3d.t ;
} with sexp
} [@@deriving sexp]
(** Read xyz coordinates of the atom *)
let of_string ~units s =

10
ocaml/Basis.ml
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@ -1,7 +1,7 @@
open Core.Std
open Sexplib.Std
open Qptypes
type t = (Gto.t * Nucl_number.t) list with sexp
type t = (Gto.t * Nucl_number.t) list [@@deriving sexp]
(** Read all the basis functions of an element *)
let read in_channel at_number =
@ -16,7 +16,7 @@ let read in_channel at_number =
(** Find an element in the basis set file *)
let find in_channel element =
In_channel.seek in_channel 0L;
seek_in in_channel 0;
let element_read = ref Element.X in
while !element_read <> element
do
@ -56,13 +56,13 @@ let to_string_general ~fmt ~atom_sep ?ele_array b =
do_work ((Gto.to_string ~fmt g)::accu) n tail
in
do_work [new_nucleus 1] 1 b
|> String.concat ~sep:"\n"
|> String.concat "\n"
let to_string_gamess ?ele_array =
to_string_general ?ele_array ~fmt:Gto.Gamess ~atom_sep:""
let to_string_gaussian ?ele_array b =
String.concat ~sep:"\n"
String.concat "\n"
[ to_string_general ?ele_array ~fmt:Gto.Gaussian ~atom_sep:"****" b ; "****" ]
let to_string ?(fmt=Gto.Gamess) =

4
ocaml/Bit.ml
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@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
(*
Type for bits
@ -11,7 +11,7 @@ Zero | One
type t =
| One
| Zero
with sexp
[@@deriving sexp]
let to_string = function
| Zero -> "0"

2
ocaml/Bit.mli
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@ -1,4 +1,4 @@
type t = One | Zero with sexp
type t = One | Zero [@@deriving sexp]
(** String conversions for printing *)
val to_string : t -> string

2
ocaml/Bitlist.ml
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@ -1,5 +1,5 @@
open Qptypes
open Core.Std
open Core
(*
Type for bits strings

4
ocaml/Charge.ml
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@ -1,6 +1,6 @@
open Core.Std
open Core
type t = float with sexp
type t = float [@@deriving sexp]
let of_float x = x
let of_int i = Float.of_int i

2
ocaml/Charge.mli
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@ -1,4 +1,4 @@
type t = float with sexp
type t = float [@@deriving sexp]
(** Float conversion functions *)
val to_float : t -> float

26
ocaml/Determinant.ml
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@ -1,7 +1,7 @@
open Core.Std;;
open Qptypes;;
open Qptypes
open Sexplib.Std
type t = int64 array with sexp
type t = int64 array [@@deriving sexp]
let to_int64_array (x:t) = (x:int64 array)
@ -9,8 +9,8 @@ let to_int64_array (x:t) = (x:int64 array)
let to_alpha_beta x =
let x = to_int64_array x in
let n_int = (Array.length x)/2 in
( Array.init n_int ~f:(fun i -> x.(i)) ,
Array.init n_int ~f:(fun i -> x.(i+n_int)) )
( Array.init n_int (fun i -> x.(i)) ,
Array.init n_int (fun i -> x.(i+n_int)) )
let to_bitlist_couple x =
@ -28,12 +28,14 @@ let bitlist_to_string ~mo_tot_num x =
let len =
MO_number.to_int mo_tot_num
in
List.map x ~f:(function
| Bit.Zero -> "-"
| Bit.One -> "+"
)
|> String.concat
|> String.sub ~pos:0 ~len
let s =
List.map (function
| Bit.Zero -> "-"
| Bit.One -> "+"
) x
|> String.concat ""
in
String.sub s 0 len
@ -77,6 +79,6 @@ let to_string ~mo_tot_num x =
let (xa,xb) = to_bitlist_couple x in
[ " " ; bitlist_to_string ~mo_tot_num xa ; "\n" ;
" " ; bitlist_to_string ~mo_tot_num xb ]
|> String.concat
|> String.concat ""

2
ocaml/Determinant.mli
View File

@ -5,7 +5,7 @@
* where each int64 is a list of 64 MOs. When the bit is set
* to 1, the MO is occupied.
*)
type t = int64 array with sexp
type t = int64 array [@@deriving sexp]
(** Transform to an int64 array *)
val to_int64_array : t -> int64 array

4
ocaml/Element.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
exception ElementError of string
@ -11,7 +11,7 @@ type t =
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
with sexp
[@@deriving sexp]
let of_string x =
match (String.capitalize (String.lowercase x)) with

2
ocaml/Element.mli
View File

@ -8,7 +8,7 @@ type t =
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
with sexp
[@@deriving sexp]
(** String conversion functions *)
val of_string : string -> t

18
ocaml/Excitation.ml
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@ -1,14 +1,14 @@
open Core.Std;;
open Qptypes;;
open Core
open Qptypes
module Hole = struct
type t = MO_class.t with sexp
type t = MO_class.t [@@deriving sexp]
let of_mo_class x = x
let to_mo_class x = x
end
module Particle = struct
type t = MO_class.t with sexp
type t = MO_class.t [@@deriving sexp]
let of_mo_class x = x
let to_mo_class x = x
end
@ -16,7 +16,7 @@ end
type t =
| Single of Hole.t*Particle.t
| Double of Hole.t*Particle.t*Hole.t*Particle.t
with sexp;;
[@@deriving sexp]
let create_single ~hole ~particle =
MO_class.(
@ -29,7 +29,7 @@ let create_single ~hole ~particle =
| ( _, Inactive _ ) -> failwith "Particles can not be in virtual MOs"
| (h, p) -> Single ( (Hole.of_mo_class h), (Particle.of_mo_class p) )
)
;;
let double_of_singles s1 s2 =
let (h1,p1) = match s1 with
@ -40,14 +40,14 @@ let double_of_singles s1 s2 =
| _ -> assert false
in
Double (h1,p1,h2,p2)
;;
let create_double ~hole1 ~particle1 ~hole2 ~particle2 =
let s1 = create_single ~hole:hole1 ~particle:particle1
and s2 = create_single ~hole:hole2 ~particle:particle2
in
double_of_singles s1 s2
;;
let to_string = function
| Single (h,p) ->
@ -68,5 +68,5 @@ let to_string = function
(MO_class.to_string (Particle.to_mo_class p2));
"]"]
|> String.concat ~sep:" "
;;

2
ocaml/Excitation.mli
View File

@ -18,7 +18,7 @@ module Particle :
type t =
| Single of Hole.t * Particle.t
| Double of Hole.t * Particle.t * Hole.t * Particle.t
with sexp
[@@deriving sexp]
val create_single : hole:MO_class.t -> particle:MO_class.t -> t

4
ocaml/GaussianPrimitive.ml
View File

@ -1,10 +1,10 @@
open Qptypes
open Core.Std
open Core
type t =
{ sym : Symmetry.t ;
expo : AO_expo.t ;
} with sexp
} [@@deriving sexp]
let to_string p =
let { sym = s ; expo = e } = p in

2
ocaml/Generic_input_of_rst.ml
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@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
open Qptypes;;

27
ocaml/Gto.ml
View File

@ -1,5 +1,5 @@
open Core.Std
open Qptypes
open Sexplib.Std
exception GTO_Read_Failure of string
exception End_Of_Basis
@ -11,11 +11,11 @@ type fmt =
type t =
{ sym : Symmetry.t ;
lc : ((GaussianPrimitive.t * AO_coef.t) list)
} with sexp
} [@@deriving sexp]
let of_prim_coef_list pc =
let (p,c) = List.hd_exn pc in
let (p,c) = List.hd pc in
let sym = p.GaussianPrimitive.sym in
let rec check = function
| [] -> `OK
@ -37,12 +37,12 @@ let of_prim_coef_list pc =
let read_one in_channel =
(* Fetch number of lines to read on first line *)
let buffer = input_line in_channel in
if ( (String.strip buffer) = "" ) then
if ( (String_ext.strip buffer) = "" ) then
raise End_Of_Basis;
let sym_str = String.sub buffer 0 2 in
let n_str = String.sub buffer 2 ((String.length buffer)-2) in
let sym = Symmetry.of_string (String.strip sym_str) in
let n = Int.of_string (String.strip n_str) in
let sym = Symmetry.of_string (String_ext.strip sym_str) in
let n = int_of_string (String_ext.strip n_str) in
(* Read all the primitives *)
let rec read_lines result = function
| 0 -> result
@ -50,18 +50,19 @@ let read_one in_channel =
begin
let line_buffer = input_line in_channel in
let buffer = line_buffer
|> String.split ~on:' '
|> List.filter ~f:(fun x -> x <> "")
|> String_ext.split ~on:' '
|> List.filter (fun x -> x <> "")
in
match buffer with
| [ j ; expo ; coef ] ->
begin
let coef = String.tr ~target:'D' ~replacement:'e' coef
let coef =
Str.global_replace (Str.regexp "D") "e" coef
in
let p =
GaussianPrimitive.of_sym_expo sym
(AO_expo.of_float (Float.of_string expo) )
and c = AO_coef.of_float (Float.of_string coef) in
(AO_expo.of_float (float_of_string expo) )
and c = AO_coef.of_float (float_of_string coef) in
read_lines ( (p,c)::result) (i-1)
end
| _ -> raise (GTO_Read_Failure line_buffer)
@ -89,7 +90,7 @@ let to_string_gamess { sym = sym ; lc = lc } =
do_work (result::accu) (i+1) tail
in
(do_work [result] 1 lc)
|> String.concat ~sep:"\n"
|> String.concat "\n"
(** Write the GTO in Gaussian format *)
@ -109,7 +110,7 @@ let to_string_gaussian { sym = sym ; lc = lc } =
do_work (result::accu) (i+1) tail
in
(do_work [result] 1 lc)
|> String.concat ~sep:"\n"
|> String.concat "\n"
(** Transform the gto to a string *)

2
ocaml/Gto.mli
View File

@ -7,7 +7,7 @@ type fmt =
type t =
{ sym : Symmetry.t ;
lc : (GaussianPrimitive.t * Qptypes.AO_coef.t) list;
} with sexp
} [@@deriving sexp]
(** Create from a list of GaussianPrimitive.t * Qptypes.AO_coef.t *)
val of_prim_coef_list :

2
ocaml/Input.ml
View File

@ -1,6 +1,6 @@
open Qputils;;
open Qptypes;;
open Core.Std;;
open Core;;
include Input_ao_basis;;
include Input_bitmasks;;

6
ocaml/Input_ao_basis.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Ao_basis : sig
type t =
@ -13,7 +13,7 @@ module Ao_basis : sig
ao_coef : AO_coef.t array;
ao_expo : AO_expo.t array;
ao_cartesian : bool;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val to_string : t -> string
@ -32,7 +32,7 @@ end = struct
ao_coef : AO_coef.t array;
ao_expo : AO_expo.t array;
ao_cartesian : bool;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "ao_basis";;

6
ocaml/Input_bi_integrals.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Bielec_integrals : sig
type t =
@ -11,7 +11,7 @@ module Bielec_integrals : sig
threshold_ao : Threshold.t;
threshold_mo : Threshold.t;
direct : bool;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val write : t -> unit
@ -27,7 +27,7 @@ end = struct
threshold_ao : Threshold.t;
threshold_mo : Threshold.t;
direct : bool;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "bielec_integrals";;

6
ocaml/Input_bitmasks.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Bitmasks : sig
type t =
@ -10,7 +10,7 @@ module Bitmasks : sig
generators : int64 array;
n_mask_cas : Bitmask_number.t;
cas : int64 array;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val to_string : t -> string
@ -22,7 +22,7 @@ end = struct
generators : int64 array;
n_mask_cas : Bitmask_number.t;
cas : int64 array;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "bitmasks";;

6
ocaml/Input_determinants_by_hand.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Determinants_by_hand : sig
type t =
@ -11,7 +11,7 @@ module Determinants_by_hand : sig
expected_s2 : Positive_float.t;
psi_coef : Det_coef.t array;
psi_det : Determinant.t array;
} with sexp
} [@@deriving sexp]
val read : unit -> t
val read_maybe : unit -> t option
val write : t -> unit
@ -30,7 +30,7 @@ end = struct
expected_s2 : Positive_float.t;
psi_coef : Det_coef.t array;
psi_det : Determinant.t array;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "determinants";;

6
ocaml/Input_electrons.ml
View File

@ -1,12 +1,12 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Electrons : sig
type t =
{ elec_alpha_num : Elec_alpha_number.t;
elec_beta_num : Elec_beta_number.t;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val write : t -> unit
@ -18,7 +18,7 @@ end = struct
type t =
{ elec_alpha_num : Elec_alpha_number.t;
elec_beta_num : Elec_beta_number.t;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "electrons";;

28
ocaml/Input_mo_basis.ml
View File

@ -1,23 +1,29 @@
open Qptypes
open Qputils
open Core.Std
open Core
type t_mo =
{ mo_tot_num : MO_number.t ;
mo_label : MO_label.t;
mo_class : MO_class.t array;
mo_occ : MO_occ.t array;
mo_coef : (MO_coef.t array) array;
ao_md5 : MD5.t;
} with sexp
module Mo_basis : sig
type t = t_mo
type t =
{ mo_tot_num : MO_number.t ;
mo_label : MO_label.t;
mo_class : MO_class.t array;
mo_occ : MO_occ.t array;
mo_coef : (MO_coef.t array) array;
ao_md5 : MD5.t;
} [@@deriving sexp]
val read : unit -> t option
val to_string : t -> string
val to_rst : t -> Rst_string.t
end = struct
type t = t_mo
type t =
{ mo_tot_num : MO_number.t ;
mo_label : MO_label.t;
mo_class : MO_class.t array;
mo_occ : MO_occ.t array;
mo_coef : (MO_coef.t array) array;
ao_md5 : MD5.t;
} [@@deriving sexp]
let get_default = Qpackage.get_ezfio_default "mo_basis"
let read_mo_label () =

6
ocaml/Input_nuclei_by_hand.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Nuclei_by_hand : sig
type t =
@ -8,7 +8,7 @@ module Nuclei_by_hand : sig
nucl_label : Element.t array;
nucl_charge : Charge.t array;
nucl_coord : Point3d.t array;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val write : t -> unit
@ -22,7 +22,7 @@ end = struct
nucl_label : Element.t array;
nucl_charge : Charge.t array;
nucl_coord : Point3d.t array;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "nuclei";;

24
ocaml/Io_ext.ml Normal file
View File

@ -0,0 +1,24 @@
let input_lines filename =
let in_channel =
open_in filename
in
let rec aux accu =
try
let newline =
input_line in_channel
in
aux (newline::accu)
with End_of_file -> accu
in
let result =
List.rev (aux [])
in
close_in in_channel;
result
let read_all filename =
input_lines filename
|> String.concat "\n"

26
ocaml/Long_basis.ml
View File

@ -1,7 +1,7 @@
open Core.Std;;
open Qptypes;;
open Qptypes
open Sexplib.Std
type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list with sexp
type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list [@@deriving sexp]
let of_basis b =
let rec do_work accu = function
@ -10,14 +10,14 @@ let of_basis b =
begin
let new_accu =
Symmetry.Xyz.of_symmetry g.Gto.sym
|> List.rev_map ~f:(fun x-> (x,g,n))
|> List.rev_map (fun x-> (x,g,n))
in
do_work (new_accu@accu) tail
end
in
do_work [] b
|> List.rev
;;
let to_basis b =
let rec do_work accu = function
@ -25,7 +25,7 @@ let to_basis b =
| (s,g,n)::tail ->
let first_sym =
Symmetry.Xyz.of_symmetry g.Gto.sym
|> List.hd_exn
|> List.hd
in
let new_accu =
if ( s = first_sym ) then
@ -36,19 +36,19 @@ let to_basis b =
do_work new_accu tail
in
do_work [] b
;;
let to_string b =
let middle = List.map ~f:(fun (x,y,z) ->
"( "^((Int.to_string (Nucl_number.to_int z)))^", "^
let middle = List.map (fun (x,y,z) ->
"( "^((string_of_int (Nucl_number.to_int z)))^", "^
(Symmetry.Xyz.to_string x)^", "^(Gto.to_string y)
^" )"
) b
|> String.concat ~sep:",\n"
|> String.concat ",\n"
in "("^middle^")"
;;
include To_md5;;
include To_md5
let to_md5 = to_md5 sexp_of_t
;;

2
ocaml/Long_basis.mli
View File

@ -5,7 +5,7 @@ open Qptypes;;
* all the D orbitals are converted to xx, xy, xz, yy, yx
* etc
*)
type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list with sexp
type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list [@@deriving sexp]
(** Transform a basis to a long basis *)
val of_basis :

4
ocaml/MO_class.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
type t =
@ -7,7 +7,7 @@ type t =
| Active of MO_number.t list
| Virtual of MO_number.t list
| Deleted of MO_number.t list
with sexp
[@@deriving sexp]
let to_string x =

2
ocaml/MO_class.mli
View File

@ -4,7 +4,7 @@ type t =
| Active of Qptypes.MO_number.t list
| Virtual of Qptypes.MO_number.t list
| Deleted of Qptypes.MO_number.t list
with sexp
[@@deriving sexp]
(** Create different excitation classes *)

4
ocaml/MO_label.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
type t =
| Guess
@ -7,7 +7,7 @@ type t =
| Localized
| Orthonormalized
| None
with sexp
[@@deriving sexp]
;;
let to_string = function

2
ocaml/MO_label.mli
View File

@ -5,7 +5,7 @@ type t =
| Localized
| Orthonormalized
| None
with sexp
[@@deriving sexp]
(** String representation *)
val to_string : t -> string

4
ocaml/Makefile
View File

@ -11,8 +11,8 @@ endif
LIBS=
PKGS=
OCAMLCFLAGS="-g -warn-error A"
OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS)
OCAMLCFLAGS="-g"
OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS)
MLLFILES=$(wildcard *.mll)
MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml Input_auto_generated.ml qp_edit.ml
MLIFILES=$(wildcard *.mli) git

2
ocaml/Message.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
(** New job : Request to create a new multi-tasked job *)

63
ocaml/Molecule.ml
View File

@ -1,14 +1,14 @@
open Core.Std ;;
open Qptypes ;;
open Qptypes
open Sexplib.Std
exception MultiplicityError of string;;
exception XYZError ;;
exception MultiplicityError of string
exception XYZError
type t = {
nuclei : Atom.t list ;
elec_alpha : Elec_alpha_number.t ;
elec_beta : Elec_beta_number.t ;
} with sexp
} [@@deriving sexp]
let get_charge { nuclei ; elec_alpha ; elec_beta } =
let result =
@ -19,7 +19,7 @@ let get_charge { nuclei ; elec_alpha ; elec_beta } =
| a::rest -> (Charge.to_float a.Atom.charge) +. nucl_charge rest
| [] -> 0.
in
Charge.of_float (nucl_charge nuclei -. (Float.of_int result))
Charge.of_float (nucl_charge nuclei -. (float_of_int result))
let get_multiplicity m =
@ -59,9 +59,10 @@ let name m =
| a::rest ->
begin
let e = a.Atom.element in
match (List.Assoc.find accu e) with
| None -> build_list (List.Assoc.add accu e 1) rest
| Some i -> build_list (List.Assoc.add accu e (i+1)) rest
try
let i = List.assoc e accu in
build_list ( (e,i+1)::(List.remove_assoc e accu) ) rest
with Not_found -> build_list ( (e,1)::accu ) rest
end
| [] -> accu
in
@ -83,7 +84,7 @@ let name m =
let result =
build_list [] nuclei |> build_name [c ; ", " ; mult]
in
String.concat (result)
String.concat "" result
let to_string_general ~f m =
@ -95,8 +96,8 @@ let to_string_general ~f m =
let title =
name m
in
[ Int.to_string n ; title ] @ (List.map ~f nuclei)
|> String.concat ~sep:"\n"
[ string_of_int n ; title ] @ (List.map f nuclei)
|> String.concat "\n"
let to_string =
to_string_general ~f:(fun x -> Atom.to_string Units.Angstrom x)
@ -109,9 +110,9 @@ let of_xyz_string
?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
?(units=Units.Angstrom)
s =
let l = String.split s ~on:'\n'
|> List.filter ~f:(fun x -> x <> "")
|> List.map ~f:(fun x -> Atom.of_string units x)
let l = String_ext.split s ~on:'\n'
|> List.filter (fun x -> x <> "")
|> List.map (fun x -> Atom.of_string units x)
in
let ne = ( get_charge {
nuclei=l ;
@ -145,25 +146,28 @@ let of_xyz_file
?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
?(units=Units.Angstrom)
filename =
let (x,buffer) = In_channel.read_all filename
|> String.lsplit2_exn ~on:'\n'
let lines =
match Io_ext.input_lines filename with
| natoms :: title :: rest ->
begin
try
if (int_of_string @@ String_ext.strip natoms) <= 0 then
raise XYZError
with
| _ -> raise XYZError
end;
String.concat "\n" rest
| _ -> raise XYZError
in
let result =
try
(int_of_string @@ String.strip x) > 0
with
| Failure "int_of_string" -> false
in
if not result then raise XYZError;
let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
of_xyz_string ~charge ~multiplicity ~units buffer
of_xyz_string ~charge:charge ~multiplicity:multiplicity
~units:units lines
let of_zmt_file
?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
?(units=Units.Angstrom)
filename =
In_channel.read_all filename
Io_ext.read_all filename
|> Zmatrix.of_string
|> Zmatrix.to_xyz_string
|> of_xyz_string ~charge ~multiplicity ~units
@ -182,14 +186,14 @@ let of_file
let distance_matrix molecule =
let coord =
molecule.nuclei
|> List.map ~f:(fun x -> x.Atom.coord)
|> List.map (fun x -> x.Atom.coord)
|> Array.of_list
in
let n =
Array.length coord
in
let result =
Array.make_matrix ~dimx:n ~dimy:n 0.
Array.make_matrix n n 0.
in
for i = 0 to (n-1)
do
@ -203,6 +207,7 @@ let distance_matrix molecule =
open Core ;;
include To_md5
let to_md5 = to_md5 sexp_of_t

2
ocaml/Molecule.mli
View File

@ -4,7 +4,7 @@ type t = {
nuclei : Atom.t list;
elec_alpha : Qptypes.Elec_alpha_number.t;
elec_beta : Qptypes.Elec_beta_number.t;
} with sexp
} [@@deriving sexp]
(** Returns the charge of the molecule *)
val get_charge : t -> Charge.t

4
ocaml/Multiplicity.ml
View File

@ -1,7 +1,7 @@
open Core.Std;;
open Core;;
open Qptypes ;;
type t = Strictly_positive_int.t with sexp
type t = Strictly_positive_int.t [@@deriving sexp]
let of_int = Strictly_positive_int.of_int ;;
let to_int = Strictly_positive_int.to_int ;;

2
ocaml/Multiplicity.mli
View File

@ -1,4 +1,4 @@
type t = Qptypes.Strictly_positive_int.t with sexp
type t = Qptypes.Strictly_positive_int.t [@@deriving sexp]
(** Conversion from int *)
val of_int : int -> t

4
ocaml/Point3d.ml
View File

@ -1,11 +1,11 @@
open Core.Std;;
open Core;;
open Qptypes;;
type t = {
x : float ;
y : float ;
z : float ;
} with sexp
} [@@deriving sexp]
let of_tuple ~units (x,y,z) =
let f = match units with

2
ocaml/Point3d.mli
View File

@ -2,7 +2,7 @@ type t =
{ x : float;
y : float;
z : float;
} with sexp
} [@@deriving sexp]
(** Create from a tuple of floats *)
val of_tuple : units:Units.units -> float*float*float -> t

2
ocaml/Primitive.mli
View File

@ -1,7 +1,7 @@
type t =
{ sym : Symmetry.t;
expo : Qptypes.AO_expo.t;
} with sexp
} [@@deriving sexp]
(** Conversion to string for printing *)
val to_string : t -> string

18
ocaml/Progress_bar.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
type t =
{
@ -53,13 +53,13 @@ let display_tty bar =
in
let stop_time =
let x =
Time.Span.to_float running_time
Time.Span.to_sec running_time
in
if (percent > 0.) then
x *. 100. /. percent -. x
|> Time.Span.of_float
|> Time.Span.of_sec
else
Time.Span.of_float 0.
Time.Span.of_sec 0.
in
Printf.eprintf "%s : [%s] %4.1f%% | %10s, ~%10s left\r%!"
bar.title
@ -67,7 +67,7 @@ let display_tty bar =
percent
(Time.Span.to_string running_time)
(stop_time |> Time.Span.to_string );
{ bar with dirty = false ; next = Time.add now (Time.Span.of_float 0.1) }
{ bar with dirty = false ; next = Time.add now (Time.Span.of_sec 0.1) }
let display_file bar =
@ -80,19 +80,19 @@ let display_file bar =
in
let stop_time =
let x =
Time.Span.to_float running_time
Time.Span.to_sec running_time
in
if (percent > 0.) then
x *. 100. /. percent -. x
|> Time.Span.of_float
|> Time.Span.of_sec
else
Time.Span.of_float 0.
Time.Span.of_sec 0.
in
Printf.eprintf "%5.2f %% in %20s, ~%20s left\n%!"
percent
(Time.Span.to_string running_time)
(Time.Span.to_string stop_time);
{ bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_float 2.) }
{ bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_sec 2.) }

12
ocaml/Pseudo.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
@ -7,7 +7,7 @@ module GaussianPrimitive_local : sig
type t = {
expo : AO_expo.t ;
r_power : R_power.t ;
} with sexp
} [@@deriving sexp]
val of_expo_r_power : AO_expo.t -> R_power.t -> t
val to_string : t -> string
@ -17,7 +17,7 @@ end = struct
type t = {
expo : AO_expo.t ;
r_power : R_power.t ;
} with sexp
} [@@deriving sexp]
let of_expo_r_power dz n =
{ expo = dz ; r_power = n }
@ -35,7 +35,7 @@ module GaussianPrimitive_non_local : sig
expo : AO_expo.t ;
r_power : R_power.t ;
proj : Positive_int.t
} with sexp
} [@@deriving sexp]
val of_proj_expo_r_power : Positive_int.t -> AO_expo.t -> R_power.t -> t
val to_string : t -> string
@ -46,7 +46,7 @@ end = struct
expo : AO_expo.t ;
r_power : R_power.t ;
proj : Positive_int.t
} with sexp
} [@@deriving sexp]
let of_proj_expo_r_power p dz n =
{ expo = dz ; r_power = n ; proj = p }
@ -66,7 +66,7 @@ type t = {
n_elec : Positive_int.t ;
local : (GaussianPrimitive_local.t * AO_coef.t ) list ;
non_local : (GaussianPrimitive_non_local.t * AO_coef.t ) list
} with sexp
} [@@deriving sexp]
let empty e =
{ element = e;

2
ocaml/Qpackage.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
open Qptypes;;
open Qputils;;

22
ocaml/Qputils.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Sexplib
(*
let rec transpose = function
@ -14,12 +14,12 @@ let rec transpose = function
let input_to_sexp s =
let result =
String.split_lines s
|> List.filter ~f:(fun x->
(String.strip x) <> "")
|> List.map ~f:(fun x->
"("^(String.tr '=' ' ' x)^")")
|> String.concat
String_ext.split ~on:'\n' s
|> List.filter (fun x-> (String_ext.strip x) <> "")
|> List.map (fun x-> "("^
(Str.global_replace (Str.regexp "=") " " x)
^")")
|> String.concat ""
in
print_endline ("("^result^")");
"("^result^")"
@ -29,10 +29,10 @@ let rmdir dirname =
let rec remove_one dir =
Sys.chdir dir;
Sys.readdir "."
|> Array.iter ~f:(fun x ->
match (Sys.is_directory x, Sys.is_file x) with
| (`Yes, _) -> remove_one x
| (_, `Yes) -> Sys.remove x
|> Array.iter (fun x ->
match (Sys.is_directory x, Sys.file_exists x) with
| (true, _) -> remove_one x
| (_, true) -> Sys.remove x
| _ -> failwith ("Unable to remove file "^x^".")
);
Sys.chdir "..";

4
ocaml/README_qp_edit.rst
View File

@ -19,7 +19,7 @@ of the block.
r_y : Y_type.t
...
last_r : bool
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t
val write : t -> unit
@ -31,7 +31,7 @@ of the block.
r_y : Y_type.t
...
last_r : bool
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "new_keyword";;

37
ocaml/Range.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Sexplib.Std
(* A range is a string of the type:
*
@ -12,14 +12,14 @@ open Core.Std;;
*)
type t = int list with sexp
type t = int list [@@deriving sexp]
let expand_range r =
match String.lsplit2 ~on:'-' r with
match String_ext.lsplit2 ~on:'-' r with
| Some (s, f) ->
begin
let start = Int.of_string s
and finish = Int.of_string f
let start = int_of_string s
and finish = int_of_string f
in
assert (start <= finish) ;
let rec do_work = function
@ -31,9 +31,9 @@ let expand_range r =
begin
match r with
| "" -> []
| _ -> [Int.of_string r]
| _ -> [int_of_string r]
end
;;
let of_string s =
match s.[0] with
@ -43,36 +43,37 @@ let of_string s =
assert (s.[0] = '[') ;
assert (s.[(String.length s)-1] = ']') ;
let s = String.sub s 1 ((String.length s) - 2) in
let l = String.split ~on:',' s in
let l = List.map ~f:expand_range l in
List.concat l |> List.dedup ~compare:Int.compare |> List.sort ~cmp:Int.compare
;;
let l = String_ext.split ~on:',' s in
let l = List.map expand_range l in
List.concat l
|> List.sort_uniq compare
let to_string l =
let rec do_work buf symbol = function
| [] -> buf
| a::([] as t) ->
do_work (buf^symbol^(Int.to_string a)) "" t
do_work (buf^symbol^(string_of_int a)) "" t
| a::(b::q as t) ->
if (b-a = 1) then
do_work buf "-" t
else
do_work (buf^symbol^(Int.to_string a)^","^(Int.to_string b)) "" t
do_work (buf^symbol^(string_of_int a)^","^(string_of_int b)) "" t
in
let result =
match l with
| [] ->
"[]"
| h::t ->
do_work ("["^(Int.to_string h)) "" l in
do_work ("["^(string_of_int h)) "" l in
(String.sub result 0 ((String.length result)))^"]"
;;
let test_module () =
let s = "[72-107,36-53,126-131]" in
let l = of_string s in
print_string s ; print_newline () ;
List.iter ~f:(fun x -> Printf.printf "%d, " x) l ; print_newline () ;
to_string l |> print_string ; print_newline () ;
;;
List.iter (fun x -> Printf.printf "%d, " x) l ; print_newline () ;
to_string l |> print_string ; print_newline ();

2
ocaml/Range.mli
View File

@ -1,4 +1,4 @@
type t = int list with sexp
type t = int list [@@deriving sexp]
(** A range is a sorted list of ints in an interval.
It is created using a string :

142
ocaml/String_ext.ml Normal file
View File

@ -0,0 +1,142 @@
include String
(** Split a string on a given character *)
let split ?(on=' ') str =
split_on_char on str
(*
let rec do_work ?(accu=[]) ?(left="") = function
| "" -> List.rev (left::accu)
| s ->
let new_s =
(length s) - 1
|> sub s 1
in
if (s.[0] = on) then
let new_accu =
left :: accu
in
do_work ~accu:new_accu new_s
else
let new_left =
concat "" [ left ; make 1 s.[0] ]
in
do_work ~accu ~left:new_left new_s
in
do_work str
*)
(** Strip blanks on the left of a string *)
let ltrim s =
let rec do_work s l =
match s.[0] with
| '\n'
| ' ' -> do_work (sub s 1 (l-1)) (l-1)
| _ -> s
in
let l =
length s
in
if (l > 0) then
do_work s l
else
s
(** Strip blanks on the right of a string *)
let rtrim s =
let rec do_work s l =
let newl =
l-1
in
match s.[newl] with
| '\n'
| ' ' -> do_work (sub s 0 (newl)) (newl)
| _ -> s
in
let l =
length s
in
if (l > 0) then
do_work s l
else
s
(** Strip blanks on the right and left of a string *)
let strip = String.trim
(** Split a string in two pieces when a character is found the 1st time from the left *)
let lsplit2_exn ?(on=' ') s =
let length =
String.length s
in
let rec do_work i =
if (i = length) then
begin
raise Not_found
end
else if (s.[i] = on) then
( String.sub s 0 i,
String.sub s (i+1) (length-i-1) )
else
do_work (i+1)
in
do_work 0
(** Split a string in two pieces when a character is found the 1st time from the right *)
let rsplit2_exn ?(on=' ') s =
let length =
String.length s
in
let rec do_work i =
if (i = -1) then
begin
raise Not_found
end
else if (s.[i] = on) then
( String.sub s 0 i,
String.sub s (i+1) (length-i-1) )
else
do_work (i-1)
in
do_work length
let lsplit2 ?(on=' ') s =
try
Some (lsplit2_exn ~on s)
with
| Not_found -> None
let rsplit2 ?(on=' ') s =
try
Some (rsplit2_exn ~on s)
with
| Not_found -> None
let to_list s =
Array.init (String.length s) (fun i -> s.[i])
|> Array.to_list
let fold ~init ~f s =
to_list s
|> List.fold_left f init
let is_prefix ~prefix s =
let len =
String.length prefix
in
if len > String.length s then
false
else
prefix = String.sub s 0 len
let of_char c =
String.make 1 c

13
ocaml/Symmetry.ml
View File

@ -1,7 +1,7 @@
open Qptypes
open Core.Std
open Sexplib.Std
type t = S|P|D|F|G|H|I|J|K|L with sexp
type t = S|P|D|F|G|H|I|J|K|L [@@deriving sexp]
let to_string = function
| S -> "S"
@ -77,7 +77,7 @@ type st = t
module Xyz = struct
type t = { x: Positive_int.t ;
y: Positive_int.t ;
z: Positive_int.t } with sexp
z: Positive_int.t } [@@deriving sexp]
type state_type = Null | X | Y | Z
(** Builds an XYZ triplet from a string.
@ -86,7 +86,7 @@ module Xyz = struct
let flush state accu number =
let n =
if (number = "") then 1
else (Int.of_string number)
else (int_of_string number)
in
match state with
| X -> { x= Positive_int.(of_int ( (to_int accu.x) +n));
@ -111,10 +111,9 @@ module Xyz = struct
| 'Z'::rest | 'z'::rest ->
let new_accu = flush state accu number in
do_work Z new_accu "" rest
| c::rest -> do_work state accu (number^(String.of_char c)) rest
| c::rest -> do_work state accu (number^(String_ext.of_char c)) rest
in
String.to_list_rev s
|> List.rev
String_ext.to_list s
|> do_work Null
{ x=Positive_int.of_int 0 ;
y=Positive_int.of_int 0 ;

4
ocaml/Symmetry.mli
View File

@ -1,4 +1,4 @@
type t = S | P | D | F | G | H | I | J | K | L with sexp
type t = S | P | D | F | G | H | I | J | K | L [@@deriving sexp]
(** Creatio from strings *)
val to_string : t -> string
@ -16,7 +16,7 @@ module Xyz :
x : Qptypes.Positive_int.t;
y : Qptypes.Positive_int.t;
z : Qptypes.Positive_int.t;
} with sexp
} [@@deriving sexp]
(** The string format contains the powers of x,y and z in a
format like "x2z3" *)

4
ocaml/TaskServer.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
@ -63,7 +63,7 @@ let bind_socket ~socket_type ~socket ~port =
ZMQ.Socket.bind socket @@ Printf.sprintf "tcp://*:%d" port;
loop (-1)
with
| Unix.Unix_error _ -> (Time.pause @@ Time.Span.of_float 1. ; loop (i-1) )
| Unix.Unix_error _ -> (Time.pause @@ Time.Span.of_sec 1. ; loop (i-1) )
| other_exception -> raise other_exception
in loop 60

4
ocaml/To_md5.ml
View File

@ -1,5 +1,5 @@
open Core.Std;;
open Qptypes;;
open Qptypes
open Sexplib
let to_md5 sexp_of_t t =
sexp_of_t t

2
ocaml/_tags
View File

@ -1,3 +1,3 @@
true: package(core,cryptokit,ZMQ,sexplib.syntax,str)
true: package(core,cryptokit,ZMQ,str,ppx_sexp_conv,ppx_deriving)
true: thread
false: profile

8
ocaml/create_git_sha1.sh
View File

@ -4,9 +4,9 @@ SHA1=$(git log -1 | head -1 | cut -d ' ' -f 2)
DATE=$(git log -1 | grep Date | cut -d ':' -f 2-)
MESSAGE=$(git log -1 | tail -1 | sed 's/"/\\"/g')
cat << EOF > Git.ml
open Core.Std
let sha1 = "$SHA1" |> String.strip
let date = "$DATE" |> String.strip
let message = "$MESSAGE" |> String.strip
open Core
let sha1 = "$SHA1" |> String_ext.strip
let date = "$DATE" |> String_ext.strip
let message = "$MESSAGE" |> String_ext.strip
EOF

2
ocaml/qp_basis_clean.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
let filenames =
let dir_name = Qpackage.root^"/data/basis/"

2
ocaml/qp_create_ezfio_from_xyz.ml
View File

@ -1,6 +1,6 @@
open Qputils
open Qptypes
open Core.Std
open Core
let spec =
let open Command.Spec in

2
ocaml/qp_create_guess.ml
View File

@ -1,6 +1,6 @@
open Qputils
open Qptypes
open Core.Std
open Core
let run ~multiplicity ezfio_file =
if (not (Sys.file_exists_exn ezfio_file)) then

109
ocaml/qp_find_pi_space.ml Normal file
View File

@ -0,0 +1,109 @@
open Core
open Qputils
open Qptypes
let run ?(sym="None") ezfio_filename =
Ezfio.set_file ezfio_filename ;
let aos =
match Input.Ao_basis.read () with
| Some aos -> aos
| None -> failwith "Unable to read AOs"
and mos =
match Input.Mo_basis.read () with
| Some mos -> mos
| None -> failwith "Unable to read MOs"
in
let rec find_power symmetry accu = function
| -1 -> accu
| i -> let new_accu =
if aos.Input.Ao_basis.ao_power.(i) = symmetry then (i::accu)
else accu
in
find_power symmetry new_accu (i-1)
and n =
(AO_number.to_int aos.Input.Ao_basis.ao_num)
and m =
(MO_number.to_int mos.Input.Mo_basis.mo_tot_num)
and one = Positive_int.of_int 1
and zero = Positive_int.of_int 0
in
(* Indices of the px, py and pz AOs *)
let x_indices =
find_power Symmetry.Xyz.{x=one ; y=zero ; z=zero} [] (n-1)
and y_indices =
find_power Symmetry.Xyz.{x=zero ; y=one ; z=zero} [] (n-1)
and z_indices =
find_power Symmetry.Xyz.{x=zero ; y=zero ; z=one } [] (n-1)
in
(* Compute the relative weight of each MO on the px, py, pz spaces *)
let compute_weight mo_i list_aos =
let num =
List.fold_left ~f:(fun s i -> s +. (MO_coef.to_float @@ mos.Input.Mo_basis.mo_coef.(mo_i).(i)) ** 2.) ~init:0. list_aos
and denom =
Array.fold ~f:(fun s x -> s +. (MO_coef.to_float x) ** 2.) ~init:0. mos.Input.Mo_basis.mo_coef.(mo_i)
in
num /. denom
in
let result =
Array.init ~f:(fun mo_i ->
(mo_i+1,
compute_weight mo_i x_indices,
compute_weight mo_i y_indices,
compute_weight mo_i z_indices) ) m
|> Array.to_list
in
let pi, sigma =
let rec aux test_xyz (accu_pi: int list) (accu_sigma: int list) = function
| [] -> (List.rev accu_pi, List.rev accu_sigma)
| (mo_i,x,y,z)::rest ->
if test_xyz (x,y,z) then
aux test_xyz (mo_i::accu_pi) accu_sigma rest
else
aux test_xyz accu_pi (mo_i::accu_sigma) rest
in
match sym with
| "x" | "X" -> aux (fun (x,y,z) -> (x>y && x>z)) [] [] result
| "y" | "Y" -> aux (fun (x,y,z) -> (y>x && y>z)) [] [] result
| "z" | "Z" -> aux (fun (x,y,z) -> (z>x && z>y)) [] [] result
| _ -> ([],[])
in
match sym with
| "x" | "X" | "y" | "Y" | "z" | "Z" ->
begin
Printf.printf "Pi: [";
List.iter ~f:(fun mo_i -> Printf.printf "%d," mo_i) pi;
Printf.printf "\b]\n\nSigma: [";
List.iter ~f:(fun mo_i -> Printf.printf "%d," mo_i) sigma;
Printf.printf "\b]\n"
end
| _ -> List.iter ~f:(fun (mo_i,x,y,z) -> Printf.printf "%d: (%f,%f,%f)\n" mo_i x y z) result
let spec =
let open Command.Spec in
empty
+> flag "sym" (optional string) ~doc:"{x,y,z} Axis perpendicular to the plane"
+> anon ("ezfio_filename" %: string)
let command =
Command.basic
~summary: "Quantum Package command"
~readme:(fun () ->
"Find all the pi molecular orbitals to create a pi space.
")
spec
(fun sym ezfio_filename () -> run ?sym ezfio_filename )
let () =
Command.run command

17
ocaml/qp_overlap_of_wf.ml
View File

@ -1,6 +1,12 @@
(**
* Computes the overlap <Psi_0 | Psi_1> where both Psi_0 and Psi_1 are truncated in the set
* of common determinants and normalized
*)
open Input_determinants_by_hand
open Qptypes
let () =
let ezfio, ezfio' =
try
@ -42,16 +48,16 @@ let () =
let overlap wf wf' =
let result, norm, norm' =
Hashtbl.fold (fun k c (accu,norm,norm') ->
let c' =
try Hashtbl.find wf' k
with Not_found -> 0.
let (c',c) =
try (Hashtbl.find wf' k, c)
with Not_found -> (0.,0.)
in
(accu +. c *. c' ,
norm +. c *. c ,
norm'+. c'*. c' )
) wf (0.,0.,0.)
in
result /. (norm *. norm')
result /. (sqrt (norm *. norm'))
in
let wf, wf' =
@ -62,5 +68,6 @@ let () =
let o =
overlap wf wf'
in
print_float (abs_float o)
print_float (abs_float o) ;
print_newline ()

2
ocaml/qp_print.ml
View File

@ -1,6 +1,6 @@
open Qputils;;
open Qptypes;;
open Core.Std;;
open Core;;
type input_action =
| Basis

2
ocaml/qp_print_basis.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
let basis () =

4
ocaml/qp_run.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qputils
(* Environment variables :
@ -132,7 +132,7 @@ let run slave exe ezfio_file =
Sys.remove qp_run_address_filename;
let duration = Time.diff (Time.now()) time_start
|> Core.Span.to_string in
|> Time.Span.to_string in
Printf.printf "Wall time : %s\n\n" duration;
if (exit_code <> 0) then
exit exit_code

6
ocaml/qp_set_mo_class.ml
View File

@ -1,6 +1,6 @@
open Qputils
open Qptypes
open Core.Std
open Core
(*
* Command-line arguments
@ -210,7 +210,7 @@ let get () =
in
let mo_tot_num =
MO_number.to_int data.Input_mo_basis.mo_tot_num
MO_number.to_int data.Input.Mo_basis.mo_tot_num
in
let n_int =
@ -244,7 +244,7 @@ let get () =
| (MO_class.Deleted _) :: rest ->
work ~del:(Printf.sprintf "%s,%d" del i) ~inact ~act ~virt ~core (i+1) rest
in
work 1 (Array.to_list data.Input_mo_basis.mo_class)
work 1 (Array.to_list data.Input.Mo_basis.mo_class)

88
ocaml/qptypes_generator.ml
View File

@ -1,4 +1,10 @@
open Core.Std;;
let global_replace x =
x
|> Str.global_replace (Str.regexp "Float.to_string") "string_of_float"
|> Str.global_replace (Str.regexp "Float.of_string") "float_of_string"
|> Str.global_replace (Str.regexp "Int.to_string") "string_of_int"
|> Str.global_replace (Str.regexp "Int.of_string") "int_of_string"
|> Str.global_replace (Str.regexp "String.\\(to\\|of\\)_string") ""
let input_data = "
* Positive_float : float
@ -118,8 +124,12 @@ let input_data = "
* MD5 : string
assert ((String.length x) = 32);
assert (String.fold x ~init:true ~f:(fun accu x ->
accu && (x < 'g')));
assert (
let a =
Array.init (String.length x) (fun i -> x.[i])
in
Array.fold_left (fun accu x -> accu && (x < 'g')) true a
);
* Rst_string : string
@ -127,7 +137,7 @@ let input_data = "
assert (x <> \"\") ;
"
;;
let input_ezfio = "
* MO_number : int
@ -156,25 +166,25 @@ let input_ezfio = "
More than 10 billion of determinants
"
;;
let untouched = "
module MO_guess : sig
type t with sexp
type t [@@deriving sexp]
val to_string : t -> string
val of_string : string -> t
end = struct
type t =
| Huckel
| HCore
with sexp
[@@deriving sexp]
let to_string = function
| Huckel -> \"Huckel\"
| HCore -> \"HCore\"
let of_string s =
match (String.lowercase s) with
match (String.lowercase_ascii s) with
| \"huckel\" -> Huckel
| \"hcore\" -> HCore
| _ -> raise (Invalid_argument (\"Wrong Guess type : \"^s))
@ -182,7 +192,7 @@ end = struct
end
module Disk_access : sig
type t with sexp
type t [@@deriving sexp]
val to_string : t -> string
val of_string : string -> t
end = struct
@ -190,14 +200,14 @@ end = struct
| Read
| Write
| None
with sexp
[@@deriving sexp]
let to_string = function
| Read -> \"Read\"
| Write -> \"Write\"
| None -> \"None\"
let of_string s =
match (String.lowercase s) with
match (String.lowercase_ascii s) with
| \"read\" -> Read
| \"write\" -> Write
| \"none\" -> None
@ -206,62 +216,63 @@ end = struct
end
"
;;
let template = format_of_string "
module %s : sig
type t with sexp
type t [@@deriving sexp]
val to_%s : t -> %s
val of_%s : %s %s -> t
val to_string : t -> string
end = struct
type t = %s with sexp
type t = %s [@@deriving sexp]
let to_%s x = x
let of_%s %s x = ( %s x )
let to_string x = %s.to_string x
end
"
;;
let parse_input input=
print_string "open Core.Std;;\nlet warning = print_string;;\n" ;
print_string "open Sexplib.Std\nlet warning = print_string\n" ;
let rec parse result = function
| [] -> result
| ( "" , "" )::tail -> parse result tail
| ( t , text )::tail ->
let name,typ,params,params_val =
match String.split ~on:':' t with
match String_ext.split ~on:':' t with
| [name;typ] -> (name,typ,"","")
| name::typ::params::params_val -> (name,typ,params,
(String.concat params_val ~sep:":") )
(String.concat ":" params_val) )
| _ -> assert false
in
let typ = String.strip typ
and name = String.strip name in
let typ = String_ext.strip typ
and name = String_ext.strip name in
let typ_cap = String.capitalize typ in
let newstring = Printf.sprintf template name typ typ typ params_val typ typ
typ typ params ( String.strip text ) typ_cap
typ typ params ( String_ext.strip text ) typ_cap
in
List.rev (parse (newstring::result) tail )
in
String.split ~on:'*' input
|> List.map ~f:(String.lsplit2_exn ~on:'\n')
String_ext.split ~on:'*' input
|> List.map (String_ext.lsplit2_exn ~on:'\n')
|> parse []
|> String.concat
|> String.concat ""
|> global_replace
|> print_string
;;
let ezfio_template = format_of_string "
module %s : sig
type t with sexp
type t [@@deriving sexp]
val to_%s : t -> %s
val get_max : unit -> %s
val of_%s : ?min:%s -> ?max:%s -> %s -> t
val to_string : t -> string
end = struct
type t = %s with sexp
type t = %s [@@deriving sexp]
let to_string x = %s.to_string x
let get_max () =
if (Ezfio.has_%s ()) then
@ -287,24 +298,24 @@ end = struct
end
end
"
;;
let parse_input_ezfio input=
let parse s =
match (
String.split s ~on:'\n'
|> List.filter ~f:(fun x -> (String.strip x) <> "")
String_ext.split s ~on:'\n'
|> List.filter (fun x -> (String_ext.strip x) <> "")
) with
| [] -> ""
| a :: b :: c :: d :: [] ->
begin
let (name,typ) = String.lsplit2_exn ~on:':' a
let (name,typ) = String_ext.lsplit2_exn ~on:':' a
and ezfio_func = b
and (min, max) = String.lsplit2_exn ~on:':' c
and (min, max) = String_ext.lsplit2_exn ~on:':' c
and msg = d
in
let (name, typ, ezfio_func, min, max, msg) =
match (List.map [ name ; typ ; ezfio_func ; min ; max ; msg ] ~f:String.strip) with
match List.map String_ext.strip [ name ; typ ; ezfio_func ; min ; max ; msg ] with
| [ name ; typ ; ezfio_func ; min ; max ; msg ] -> (name, typ, ezfio_func, min, max, msg)
| _ -> assert false
in
@ -314,16 +325,17 @@ let parse_input_ezfio input=
end
| _ -> failwith "Error in input_ezfio"
in
String.split ~on:'*' input
|> List.map ~f:parse
|> String.concat
String_ext.split ~on:'*' input
|> List.map parse
|> String.concat ""
|> global_replace
|> print_string
;;
let () =
parse_input input_data ;
parse_input_ezfio input_ezfio;
print_endline untouched;
print_endline untouched

2
ocaml/test_basis.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
open Qputils;;
open Qptypes;;

2
ocaml/test_gto.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
let test_prim () =

2
ocaml/test_message.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
let () =
Message.of_string "new_job ao_integrals tcp://127.0.0.1 inproc://ao_ints:12345"

2
ocaml/test_molecule.ml
View File

@ -1,4 +1,4 @@
open Core.Std ;;
open Core ;;
open Qptypes ;;
let test_molecule () =

2
ocaml/test_pseudo.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qputils
open Qptypes

2
ocaml/test_queuing_system.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
let () =

10
ocaml/test_symmetry.ml
View File

@ -1,15 +1,13 @@
open Core.Std
open Qputils
open Qptypes
open Symmetry
let () =
"SPDFGHIJKL"
|> String.to_list_rev
|> List.rev
|> List.map ~f:of_char
|> List.map ~f:Xyz.of_symmetry
|> List.iter ~f:(fun x -> List.iter x ~f:(fun y -> Xyz.to_string y |> print_endline) ;
|> String_ext.to_list
|> List.map of_char
|> List.map Xyz.of_symmetry
|> List.iter (fun x -> List.iter (fun y -> Xyz.to_string y |> print_endline) x ;
print_newline ();)

2
ocaml/test_task_server.ml
View File

@ -1,5 +1,3 @@
open Core
let () =
TaskServer.run 12345

74
plugins/CAS_SD_ZMQ/selection.irp.f
View File

@ -1,28 +1,6 @@
use bitmasks
double precision function integral8(i,j,k,l)
implicit none
integer, intent(in) :: i,j,k,l
double precision, external :: get_mo_bielec_integral
integer :: ii
ii = l-mo_integrals_cache_min
ii = ior(ii, k-mo_integrals_cache_min)
ii = ior(ii, j-mo_integrals_cache_min)
ii = ior(ii, i-mo_integrals_cache_min)
if (iand(ii, -64) /= 0) then
integral8 = get_mo_bielec_integral(i,j,k,l,mo_integrals_map)
else
ii = l-mo_integrals_cache_min
ii = ior( ishft(ii,6), k-mo_integrals_cache_min)
ii = ior( ishft(ii,6), j-mo_integrals_cache_min)
ii = ior( ishft(ii,6), i-mo_integrals_cache_min)
integral8 = mo_integrals_cache(ii)
endif
end function
BEGIN_PROVIDER [ integer(1), psi_phasemask, (N_int*bit_kind_size, 2, N_det)]
use bitmasks
implicit none
@ -287,7 +265,7 @@ subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
integer, intent(in) :: sp, h(0:2, 2), p(0:3, 2)
integer :: i, j, h1, h2, p1, p2, sfix, hfix, pfix, hmob, pmob, puti
double precision :: hij
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
integer, parameter :: turn3_2(2,3) = reshape((/2,3, 1,3, 1,2/), (/2,3/))
integer, parameter :: turn2(2) = (/2,1/)
@ -300,7 +278,7 @@ subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
if(bannedOrb(puti)) cycle
p1 = p(turn3_2(1,i), sp)
p2 = p(turn3_2(2,i), sp)
hij = integral8(p1, p2, h1, h2) - integral8(p2, p1, h1, h2)
hij = mo_bielec_integral(p1, p2, h1, h2) - mo_bielec_integral(p2, p1, h1, h2)
hij *= get_phase_bi(phasemask, sp, sp, h1, p1, h2, p2)
vect(:, puti) += hij * coefs
end do
@ -313,7 +291,7 @@ subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
puti = p(j, sp)
if(bannedOrb(puti)) cycle
pmob = p(turn2(j), sp)
hij = integral8(pfix, pmob, hfix, hmob)
hij = mo_bielec_integral(pfix, pmob, hfix, hmob)
hij *= get_phase_bi(phasemask, sp, sfix, hmob, pmob, hfix, pfix)
vect(:, puti) += hij * coefs
end do
@ -325,7 +303,7 @@ subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
p2 = p(2,sfix)
h1 = h(1,sfix)
h2 = h(2,sfix)
hij = (integral8(p1,p2,h1,h2) - integral8(p2,p1,h1,h2))
hij = (mo_bielec_integral(p1,p2,h1,h2) - mo_bielec_integral(p2,p1,h1,h2))
hij *= get_phase_bi(phasemask, sfix, sfix, h1, p1, h2, p2)
vect(:, puti) += hij * coefs
end if
@ -348,7 +326,7 @@ subroutine get_m1(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
logical :: ok, lbanned(mo_tot_num)
integer(bit_kind) :: det(N_int, 2)
double precision :: hij
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
lbanned = bannedOrb
sh = 1
@ -366,13 +344,13 @@ subroutine get_m1(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
do i=1,hole-1
if(lbanned(i)) cycle
hij = (integral8(p1, p2, i, hole) - integral8(p2, p1, i, hole))
hij = (mo_bielec_integral(p1, p2, i, hole) - mo_bielec_integral(p2, p1, i, hole))
hij *= get_phase_bi(phasemask, sp, sp, i, p1, hole, p2)
vect(:,i) += hij * coefs
end do
do i=hole+1,mo_tot_num
if(lbanned(i)) cycle
hij = (integral8(p1, p2, hole, i) - integral8(p2, p1, hole, i))
hij = (mo_bielec_integral(p1, p2, hole, i) - mo_bielec_integral(p2, p1, hole, i))
hij *= get_phase_bi(phasemask, sp, sp, hole, p1, i, p2)
vect(:,i) += hij * coefs
end do
@ -384,7 +362,7 @@ subroutine get_m1(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
p2 = p(1, sh)
do i=1,mo_tot_num
if(lbanned(i)) cycle
hij = integral8(p1, p2, i, hole)
hij = mo_bielec_integral(p1, p2, i, hole)
hij *= get_phase_bi(phasemask, sp, sh, i, p1, hole, p2)
vect(:,i) += hij * coefs
end do
@ -787,7 +765,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
double precision, intent(inout) :: mat(N_states, mo_tot_num, mo_tot_num)
integer, intent(in) :: h(0:2,2), p(0:4,2), sp
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
integer :: i, j, tip, ma, mi, puti, putj
integer :: h1, h2, p1, p2, i1, i2
@ -822,7 +800,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
h1 = h(1, ma)
h2 = h(2, ma)
hij = (integral8(p1, p2, h1, h2) - integral8(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2)
hij = (mo_bielec_integral(p1, p2, h1, h2) - mo_bielec_integral(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2)
if(ma == 1) then
mat(:, putj, puti) += coefs * hij
else
@ -841,7 +819,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
h1 = h(1,1)
h2 = h(1,2)
hij = integral8(p1, p2, h1, h2) * get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2)
hij = mo_bielec_integral(p1, p2, h1, h2) * get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2)
mat(:, puti, putj) += coefs * hij
end do
end do
@ -861,7 +839,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
i2 = turn2d(2, i, j)
p1 = p(i1, ma)
p2 = p(i2, ma)
hij = (integral8(p1, p2, h1, h2) - integral8(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2)
hij = (mo_bielec_integral(p1, p2, h1, h2) - mo_bielec_integral(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2)
mat(:, puti, putj) += coefs * hij
end do
end do
@ -875,7 +853,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
if(banned(puti,putj,1)) cycle
p2 = p(i, ma)
hij = integral8(p1, p2, h1, h2) * get_phase_bi(phasemask, mi, ma, h1, p1, h2, p2)
hij = mo_bielec_integral(p1, p2, h1, h2) * get_phase_bi(phasemask, mi, ma, h1, p1, h2, p2)
mat(:, min(puti, putj), max(puti, putj)) += coefs * hij
end do
else ! tip == 4
@ -886,7 +864,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
p2 = p(2, mi)
h1 = h(1, mi)
h2 = h(2, mi)
hij = (integral8(p1, p2, h1, h2) - integral8(p2,p1, h1, h2)) * get_phase_bi(phasemask, mi, mi, h1, p1, h2, p2)
hij = (mo_bielec_integral(p1, p2, h1, h2) - mo_bielec_integral(p2,p1, h1, h2)) * get_phase_bi(phasemask, mi, mi, h1, p1, h2, p2)
mat(:, puti, putj) += coefs * hij
end if
end if
@ -905,7 +883,7 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
double precision, intent(in) :: coefs(N_states)
double precision, intent(inout) :: mat(N_states, mo_tot_num, mo_tot_num)
double precision :: hij, tmp_row(N_states, mo_tot_num), tmp_row2(N_states, mo_tot_num)
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
logical :: lbanned(mo_tot_num, 2), ok
integer :: puti, putj, ma, mi, s1, s2, i, i1, i2, j, hfix, pfix, h1, h2, p1, p2, ib
@ -944,12 +922,12 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
tmp_row = 0d0
do putj=1, hfix-1
if(lbanned(putj, ma) .or. banned(putj, puti,bant)) cycle
hij = (integral8(p1, p2, putj, hfix)-integral8(p2,p1,putj,hfix)) * get_phase_bi(phasemask, ma, ma, putj, p1, hfix, p2)
hij = (mo_bielec_integral(p1, p2, putj, hfix)-mo_bielec_integral(p2,p1,putj,hfix)) * get_phase_bi(phasemask, ma, ma, putj, p1, hfix, p2)
tmp_row(1:N_states,putj) += hij * coefs(1:N_states)
end do
do putj=hfix+1, mo_tot_num
if(lbanned(putj, ma) .or. banned(putj, puti,bant)) cycle
hij = (integral8(p1, p2, hfix, putj)-integral8(p2,p1,hfix,putj)) * get_phase_bi(phasemask, ma, ma, hfix, p1, putj, p2)
hij = (mo_bielec_integral(p1, p2, hfix, putj)-mo_bielec_integral(p2,p1,hfix,putj)) * get_phase_bi(phasemask, ma, ma, hfix, p1, putj, p2)
tmp_row(1:N_states,putj) += hij * coefs(1:N_states)
end do
@ -969,13 +947,13 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
!p1 fixed
putj = p1
if(.not. banned(putj,puti,bant)) then
hij = integral8(p2,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p2, puti, pfix)
hij = mo_bielec_integral(p2,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p2, puti, pfix)
tmp_row(:,puti) += hij * coefs
end if
putj = p2
if(.not. banned(putj,puti,bant)) then
hij = integral8(p1,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p1, puti, pfix)
hij = mo_bielec_integral(p1,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p1, puti, pfix)
tmp_row2(:,puti) += hij * coefs
end if
end do
@ -997,12 +975,12 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
tmp_row = 0d0
do putj=1,hfix-1
if(lbanned(putj,ma) .or. banned(puti,putj,1)) cycle
hij = (integral8(p1, p2, putj, hfix)-integral8(p2,p1,putj,hfix)) * get_phase_bi(phasemask, ma, ma, putj, p1, hfix, p2)
hij = (mo_bielec_integral(p1, p2, putj, hfix)-mo_bielec_integral(p2,p1,putj,hfix)) * get_phase_bi(phasemask, ma, ma, putj, p1, hfix, p2)
tmp_row(:,putj) += hij * coefs
end do
do putj=hfix+1,mo_tot_num
if(lbanned(putj,ma) .or. banned(puti,putj,1)) cycle
hij = (integral8(p1, p2, hfix, putj)-integral8(p2,p1,hfix,putj)) * get_phase_bi(phasemask, ma, ma, hfix, p1, putj, p2)
hij = (mo_bielec_integral(p1, p2, hfix, putj)-mo_bielec_integral(p2,p1,hfix,putj)) * get_phase_bi(phasemask, ma, ma, hfix, p1, putj, p2)
tmp_row(:,putj) += hij * coefs
end do
@ -1020,13 +998,13 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
if(lbanned(puti,ma)) cycle
putj = p2
if(.not. banned(puti,putj,1)) then
hij = integral8(pfix, p1, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p1)
hij = mo_bielec_integral(pfix, p1, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p1)
tmp_row(:,puti) += hij * coefs
end if
putj = p1
if(.not. banned(puti,putj,1)) then
hij = integral8(pfix, p2, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p2)
hij = mo_bielec_integral(pfix, p2, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p2)
tmp_row2(:,puti) += hij * coefs
end if
end do
@ -1077,7 +1055,7 @@ subroutine get_d0(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
integer :: i, j, s, h1, h2, p1, p2, puti, putj
double precision :: hij, phase
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
logical :: ok
integer :: bant
@ -1096,7 +1074,7 @@ subroutine get_d0(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
call apply_particles(mask, 1,p1,2,p2, det, ok, N_int)
call i_h_j(gen, det, N_int, hij)
else
hij = integral8(p1, p2, h1, h2) * get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2)
hij = mo_bielec_integral(p1, p2, h1, h2) * get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2)
phase = get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2)
end if
mat(:, p1, p2) += coefs(:) * hij
@ -1114,7 +1092,7 @@ subroutine get_d0(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
call apply_particles(mask, sp,puti,sp,putj, det, ok, N_int)
call i_h_j(gen, det, N_int, hij)
else
hij = (integral8(p1, p2, puti, putj) - integral8(p2, p1, puti, putj))* get_phase_bi(phasemask, sp, sp, puti, p1 , putj, p2)
hij = (mo_bielec_integral(p1, p2, puti, putj) - mo_bielec_integral(p2, p1, puti, putj))* get_phase_bi(phasemask, sp, sp, puti, p1 , putj, p2)
end if
mat(:, puti, putj) += coefs(:) * hij
end do

4
plugins/FOBOCI/diag_fock_inactiv_virt.irp.f
View File

@ -29,7 +29,7 @@ subroutine diag_inactive_virt_and_update_mos
label = "Canonical"
call mo_as_eigvectors_of_mo_matrix(tmp,size(tmp,1),size(tmp,2),label,1)
call mo_as_eigvectors_of_mo_matrix(tmp,size(tmp,1),size(tmp,2),label,1,.false.)
soft_touch mo_coef
@ -76,7 +76,7 @@ subroutine diag_inactive_virt_new_and_update_mos
label = "Canonical"
call mo_as_eigvectors_of_mo_matrix(tmp,size(tmp,1),size(tmp,2),label,1)
call mo_as_eigvectors_of_mo_matrix(tmp,size(tmp,1),size(tmp,2),label,1,.false.)
soft_touch mo_coef

2
plugins/FOBOCI/new_approach.irp.f
View File

@ -655,7 +655,7 @@ subroutine new_approach
integer :: sign
sign = -1
call mo_as_eigvectors_of_mo_matrix(one_body_dm_mo,size(one_body_dm_mo,1),size(one_body_dm_mo,2),label,sign)
call mo_as_eigvectors_of_mo_matrix(one_body_dm_mo,size(one_body_dm_mo,1),size(one_body_dm_mo,2),label,sign,.true.)
soft_touch mo_coef
call save_mos

4
plugins/FOBOCI/routines_foboci.irp.f
View File

@ -449,7 +449,7 @@ subroutine save_osoci_natural_mos
label = "Natural"
call mo_as_eigvectors_of_mo_matrix(tmp,size(tmp,1),size(tmp,2),label,1)
call mo_as_eigvectors_of_mo_matrix(tmp,size(tmp,1),size(tmp,2),label,1,.true.)
!if(disk_access_ao_integrals == "None" .or. disk_access_ao_integrals == "Write" )then
! disk_access_ao_integrals = "Read"
! touch disk_access_ao_integrals
@ -584,7 +584,7 @@ subroutine set_osoci_natural_mos
enddo
label = "Natural"
call mo_as_eigvectors_of_mo_matrix(tmp,size(tmp,1),size(tmp,2),label,1)
call mo_as_eigvectors_of_mo_matrix(tmp,size(tmp,1),size(tmp,2),label,1,.true.)
soft_touch mo_coef
deallocate(tmp,occ)

75
plugins/Full_CI_ZMQ/selection.irp.f
View File

@ -9,29 +9,6 @@ BEGIN_PROVIDER [ integer, fragment_count ]
END_PROVIDER
double precision function integral8(i,j,k,l)
implicit none
integer, intent(in) :: i,j,k,l
double precision, external :: get_mo_bielec_integral
integer :: ii
ii = l-mo_integrals_cache_min
ii = ior(ii, k-mo_integrals_cache_min)
ii = ior(ii, j-mo_integrals_cache_min)
ii = ior(ii, i-mo_integrals_cache_min)
if (iand(ii, -64) /= 0) then
integral8 = get_mo_bielec_integral(i,j,k,l,mo_integrals_map)
else
ii = l-mo_integrals_cache_min
ii = ior( ishft(ii,6), k-mo_integrals_cache_min)
ii = ior( ishft(ii,6), j-mo_integrals_cache_min)
ii = ior( ishft(ii,6), i-mo_integrals_cache_min)
integral8 = mo_integrals_cache(ii)
endif
end function
subroutine assert(cond, msg)
character(*), intent(in) :: msg
logical, intent(in) :: cond
@ -135,7 +112,7 @@ subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
integer, intent(in) :: sp, h(0:2, 2), p(0:3, 2)
integer :: i, j, h1, h2, p1, p2, sfix, hfix, pfix, hmob, pmob, puti
double precision :: hij
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
integer, parameter :: turn3_2(2,3) = reshape((/2,3, 1,3, 1,2/), (/2,3/))
integer, parameter :: turn2(2) = (/2,1/)
@ -148,7 +125,7 @@ subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
if(bannedOrb(puti)) cycle
p1 = p(turn3_2(1,i), sp)
p2 = p(turn3_2(2,i), sp)
hij = integral8(p1, p2, h1, h2) - integral8(p2, p1, h1, h2)
hij = mo_bielec_integral(p1, p2, h1, h2) - mo_bielec_integral(p2, p1, h1, h2)
hij *= get_phase_bi(phasemask, sp, sp, h1, p1, h2, p2)
vect(:, puti) += hij * coefs
end do
@ -161,7 +138,7 @@ subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
puti = p(j, sp)
if(bannedOrb(puti)) cycle
pmob = p(turn2(j), sp)
hij = integral8(pfix, pmob, hfix, hmob)
hij = mo_bielec_integral(pfix, pmob, hfix, hmob)
hij *= get_phase_bi(phasemask, sp, sfix, hmob, pmob, hfix, pfix)
vect(:, puti) += hij * coefs
end do
@ -173,7 +150,7 @@ subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
p2 = p(2,sfix)
h1 = h(1,sfix)
h2 = h(2,sfix)
hij = (integral8(p1,p2,h1,h2) - integral8(p2,p1,h1,h2))
hij = (mo_bielec_integral(p1,p2,h1,h2) - mo_bielec_integral(p2,p1,h1,h2))
hij *= get_phase_bi(phasemask, sfix, sfix, h1, p1, h2, p2)
vect(:, puti) += hij * coefs
end if
@ -198,7 +175,7 @@ subroutine get_m1(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
logical, allocatable :: lbanned(:)
integer(bit_kind) :: det(N_int, 2)
double precision :: hij
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
allocate (lbanned(mo_tot_num))
lbanned = bannedOrb
@ -217,13 +194,13 @@ subroutine get_m1(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
do i=1,hole-1
if(lbanned(i)) cycle
hij = (integral8(p1, p2, i, hole) - integral8(p2, p1, i, hole))
hij = (mo_bielec_integral(p1, p2, i, hole) - mo_bielec_integral(p2, p1, i, hole))
hij *= get_phase_bi(phasemask, sp, sp, i, p1, hole, p2)
vect(1:N_states,i) += hij * coefs(1:N_states)
end do
do i=hole+1,mo_tot_num
if(lbanned(i)) cycle
hij = (integral8(p1, p2, hole, i) - integral8(p2, p1, hole, i))
hij = (mo_bielec_integral(p1, p2, hole, i) - mo_bielec_integral(p2, p1, hole, i))
hij *= get_phase_bi(phasemask, sp, sp, hole, p1, i, p2)
vect(1:N_states,i) += hij * coefs(1:N_states)
end do
@ -235,7 +212,7 @@ subroutine get_m1(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
p2 = p(1, sh)
do i=1,mo_tot_num
if(lbanned(i)) cycle
hij = integral8(p1, p2, i, hole)
hij = mo_bielec_integral(p1, p2, i, hole)
hij *= get_phase_bi(phasemask, sp, sh, i, p1, hole, p2)
vect(1:N_states,i) += hij * coefs(1:N_states)
end do
@ -722,7 +699,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
double precision, intent(inout) :: mat(N_states, mo_tot_num, mo_tot_num)
integer, intent(in) :: h(0:2,2), p(0:4,2), sp
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
integer :: i, j, tip, ma, mi, puti, putj
integer :: h1, h2, p1, p2, i1, i2
@ -757,7 +734,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
h1 = h(1, ma)
h2 = h(2, ma)
hij = (integral8(p1, p2, h1, h2) - integral8(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2)
hij = (mo_bielec_integral(p1, p2, h1, h2) - mo_bielec_integral(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2)
if(ma == 1) then
mat(:, putj, puti) += coefs * hij
else
@ -776,7 +753,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
if(banned(puti,putj,bant)) cycle
p1 = p(turn2(i), 1)
hij = integral8(p1, p2, h1, h2) * get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2)
hij = mo_bielec_integral(p1, p2, h1, h2) * get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2)
mat(:, puti, putj) += coefs * hij
end do
end do
@ -796,7 +773,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
i2 = turn2d(2, i, j)
p1 = p(i1, ma)
p2 = p(i2, ma)
hij = (integral8(p1, p2, h1, h2) - integral8(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2)
hij = (mo_bielec_integral(p1, p2, h1, h2) - mo_bielec_integral(p2,p1, h1, h2)) * get_phase_bi(phasemask, ma, ma, h1, p1, h2, p2)
mat(:, puti, putj) += coefs * hij
end do
end do
@ -810,7 +787,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
if(banned(puti,putj,1)) cycle
p2 = p(i, ma)
hij = integral8(p1, p2, h1, h2) * get_phase_bi(phasemask, mi, ma, h1, p1, h2, p2)
hij = mo_bielec_integral(p1, p2, h1, h2) * get_phase_bi(phasemask, mi, ma, h1, p1, h2, p2)
mat(:, min(puti, putj), max(puti, putj)) += coefs * hij
end do
else ! tip == 4
@ -821,7 +798,7 @@ subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
p2 = p(2, mi)
h1 = h(1, mi)
h2 = h(2, mi)
hij = (integral8(p1, p2, h1, h2) - integral8(p2,p1, h1, h2)) * get_phase_bi(phasemask, mi, mi, h1, p1, h2, p2)
hij = (mo_bielec_integral(p1, p2, h1, h2) - mo_bielec_integral(p2,p1, h1, h2)) * get_phase_bi(phasemask, mi, mi, h1, p1, h2, p2)
mat(:, puti, putj) += coefs * hij
end if
end if
@ -841,7 +818,7 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
double precision, intent(inout) :: mat(N_states, mo_tot_num, mo_tot_num)
integer, intent(in) :: h(0:2,2), p(0:4,2), sp
double precision :: hij, tmp_row(N_states, mo_tot_num), tmp_row2(N_states, mo_tot_num)
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
logical :: ok
logical, allocatable :: lbanned(:,:)
@ -881,12 +858,12 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
tmp_row = 0d0
do putj=1, hfix-1
if(lbanned(putj, ma) .or. banned(putj, puti,bant)) cycle
hij = (integral8(p1, p2, putj, hfix)-integral8(p2,p1,putj,hfix)) * get_phase_bi(phasemask, ma, ma, putj, p1, hfix, p2)
hij = (mo_bielec_integral(p1, p2, putj, hfix)-mo_bielec_integral(p2,p1,putj,hfix)) * get_phase_bi(phasemask, ma, ma, putj, p1, hfix, p2)
tmp_row(1:N_states,putj) += hij * coefs(1:N_states)
end do
do putj=hfix+1, mo_tot_num
if(lbanned(putj, ma) .or. banned(putj, puti,bant)) cycle
hij = (integral8(p1, p2, hfix, putj)-integral8(p2,p1,hfix,putj)) * get_phase_bi(phasemask, ma, ma, hfix, p1, putj, p2)
hij = (mo_bielec_integral(p1, p2, hfix, putj)-mo_bielec_integral(p2,p1,hfix,putj)) * get_phase_bi(phasemask, ma, ma, hfix, p1, putj, p2)
tmp_row(1:N_states,putj) += hij * coefs(1:N_states)
end do
@ -906,13 +883,13 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
!p1 fixed
putj = p1
if(.not. banned(putj,puti,bant)) then
hij = integral8(p2,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p2, puti, pfix)
hij = mo_bielec_integral(p2,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p2, puti, pfix)
tmp_row(:,puti) += hij * coefs
end if
putj = p2
if(.not. banned(putj,puti,bant)) then
hij = integral8(p1,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p1, puti, pfix)
hij = mo_bielec_integral(p1,pfix,hfix,puti) * get_phase_bi(phasemask, ma, mi, hfix, p1, puti, pfix)
tmp_row2(:,puti) += hij * coefs
end if
end do
@ -934,12 +911,12 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
tmp_row = 0d0
do putj=1,hfix-1
if(lbanned(putj,ma) .or. banned(puti,putj,1)) cycle
hij = (integral8(p1, p2, putj, hfix)-integral8(p2,p1,putj,hfix)) * get_phase_bi(phasemask, ma, ma, putj, p1, hfix, p2)
hij = (mo_bielec_integral(p1, p2, putj, hfix)-mo_bielec_integral(p2,p1,putj,hfix)) * get_phase_bi(phasemask, ma, ma, putj, p1, hfix, p2)
tmp_row(:,putj) += hij * coefs
end do
do putj=hfix+1,mo_tot_num
if(lbanned(putj,ma) .or. banned(puti,putj,1)) cycle
hij = (integral8(p1, p2, hfix, putj)-integral8(p2,p1,hfix,putj)) * get_phase_bi(phasemask, ma, ma, hfix, p1, putj, p2)
hij = (mo_bielec_integral(p1, p2, hfix, putj)-mo_bielec_integral(p2,p1,hfix,putj)) * get_phase_bi(phasemask, ma, ma, hfix, p1, putj, p2)
tmp_row(:,putj) += hij * coefs
end do
@ -957,13 +934,13 @@ subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
if(lbanned(puti,ma)) cycle
putj = p2
if(.not. banned(puti,putj,1)) then
hij = integral8(pfix, p1, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p1)
hij = mo_bielec_integral(pfix, p1, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p1)
tmp_row(:,puti) += hij * coefs
end if
putj = p1
if(.not. banned(puti,putj,1)) then
hij = integral8(pfix, p2, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p2)
hij = mo_bielec_integral(pfix, p2, hfix, puti) * get_phase_bi(phasemask, mi, ma, hfix, pfix, puti, p2)
tmp_row2(:,puti) += hij * coefs
end if
end do
@ -1015,7 +992,7 @@ subroutine get_d0(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
integer :: i, j, s, h1, h2, p1, p2, puti, putj
double precision :: hij, phase
double precision, external :: get_phase_bi, integral8
double precision, external :: get_phase_bi, mo_bielec_integral
logical :: ok
integer :: bant
@ -1035,7 +1012,7 @@ subroutine get_d0(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
call i_h_j(gen, det, N_int, hij)
else
phase = get_phase_bi(phasemask, 1, 2, h1, p1, h2, p2)
hij = integral8(p1, p2, h1, h2) * phase
hij = mo_bielec_integral(p1, p2, h1, h2) * phase
end if
mat(:, p1, p2) += coefs(:) * hij
end do
@ -1052,7 +1029,7 @@ subroutine get_d0(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
call apply_particles(mask, sp,puti,sp,putj, det, ok, N_int)
call i_h_j(gen, det, N_int, hij)
else
hij = (integral8(p1, p2, puti, putj) - integral8(p2, p1, puti, putj))* get_phase_bi(phasemask, sp, sp, puti, p1 , putj, p2)
hij = (mo_bielec_integral(p1, p2, puti, putj) - mo_bielec_integral(p2, p1, puti, putj))* get_phase_bi(phasemask, sp, sp, puti, p1 , putj, p2)
end if
mat(:, puti, putj) += coefs(:) * hij
end do

3
plugins/Full_CI_ZMQ/selection_slave.irp.f
View File

@ -19,13 +19,14 @@ end
subroutine run_wf
use f77_zmq
implicit none
integer(ZMQ_PTR), external :: new_zmq_to_qp_run_socket
integer(ZMQ_PTR) :: zmq_to_qp_run_socket
double precision :: energy(N_states)
character*(64) :: states(4)
integer :: rc, i
integer :: rc, i, ierr
call provide_everything

1
plugins/Full_CI_ZMQ_GPI2/NEEDED_CHILDREN_MODULES Normal file
View File

@ -0,0 +1 @@
Full_CI_ZMQ GPI2

9
plugins/Full_CI_ZMQ_MPI/README.rst → plugins/Full_CI_ZMQ_GPI2/README.rst
View File

@ -1,8 +1,9 @@
===============
Full_CI_ZMQ_MPI
===============
================
Full_CI_ZMQ_GPI2
================
MPI Slave for Full_CI with ZMQ
GPI2 Slave for Full_CI with ZMQ. There should be one instance of the slave
per compute node.
Needed Modules
==============

18
plugins/Full_CI_ZMQ_MPI/selection_davidson_slave_mpi.irp.f → plugins/Full_CI_ZMQ_GPI2/selection_davidson_slave_gpi2.irp.f
View File

@ -14,7 +14,7 @@ end
subroutine provide_everything
PROVIDE H_apply_buffer_allocated mo_bielec_integrals_in_map psi_det_generators psi_coef_generators psi_det_sorted_bit psi_selectors n_det_generators n_states generators_bitmask zmq_context
PROVIDE pt2_e0_denominator mo_tot_num N_int fragment_count MPI_Initialized
PROVIDE pt2_e0_denominator mo_tot_num N_int fragment_count GASPI_is_Initialized
end
subroutine run_wf
@ -51,12 +51,10 @@ subroutine run_wf
! ---------
print *, 'Selection'
if (is_mpi_master) then
if (is_gaspi_master) then
call zmq_get_psi(zmq_to_qp_run_socket,1,energy,N_states)
endif
IRP_IF MIP
call MPI_BCAST(n,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
IRP_ENDIF
call broadcast_wf(energy)
!$OMP PARALLEL PRIVATE(i)
i = omp_get_thread_num()
@ -70,7 +68,10 @@ subroutine run_wf
! --------
print *, 'Davidson'
call zmq_get_psi(zmq_to_qp_run_socket,1,energy,N_states)
if (is_gaspi_master) then
call zmq_get_psi(zmq_to_qp_run_socket,1,energy,N_states)
endif
call broadcast_wf(energy)
call omp_set_nested(.True.)
call davidson_slave_tcp(0)
call omp_set_nested(.False.)
@ -82,7 +83,10 @@ subroutine run_wf
! ---
print *, 'PT2'
call zmq_get_psi(zmq_to_qp_run_socket,1,energy,N_states)
if (is_gaspi_master) then
call zmq_get_psi(zmq_to_qp_run_socket,1,energy,N_states)
endif
call broadcast_wf(energy)
logical :: lstop
lstop = .False.

1
plugins/Full_CI_ZMQ_MPI/NEEDED_CHILDREN_MODULES
View File

@ -1 +0,0 @@
Full_CI_ZMQ MPI

1
plugins/GPI2/NEEDED_CHILDREN_MODULES Normal file
View File

@ -0,0 +1 @@
Determinants

8
plugins/MPI/README.rst → plugins/GPI2/README.rst
View File

@ -1,8 +1,8 @@
===
MPI
===
=====
GASPI
=====
Providers for MPI programs.
Providers for GASPI programs (with the GPI2 library).
Needed Modules
==============

13
plugins/GPI2/gpi_test.irp.f Normal file
View File

@ -0,0 +1,13 @@
program test
double precision :: energy(N_states)
if (is_gaspi_master) then
energy = 1.d0
else
energy = 0.d0
endif
call broadcast_wf(energy)
print *, 'energy (1.d0) :', GASPI_rank, energy(1)
print *, 'coef :', GASPI_rank, psi_coef(1,1)
print *, 'det :', GASPI_rank, psi_det (1,1,1)
call gaspi_finalize
end

76
plugins/GPI2/utils.irp.f Normal file
View File

@ -0,0 +1,76 @@
BEGIN_PROVIDER [ logical, GASPI_is_initialized ]
&BEGIN_PROVIDER [ logical, has_gaspi ]
implicit none
BEGIN_DOC
! This is true when GASPI_Init has been called
END_DOC
has_gaspi = .False.
IRP_IF GASPI
use GASPI
integer(gaspi_return_t) :: res
res = gaspi_proc_init(GASPI_BLOCK)
if (res /= GASPI_SUCCESS) then
print *, res
print *, 'GASPI failed to initialize'
stop -1
endif
has_gaspi = .True.
IRP_ENDIF
GASPI_is_initialized = .True.
END_PROVIDER
BEGIN_PROVIDER [ integer, GASPI_rank ]
&BEGIN_PROVIDER [ integer, GASPI_size ]
&BEGIN_PROVIDER [ logical, is_GASPI_master ]
implicit none
BEGIN_DOC
! Usual GASPI variables
END_DOC
PROVIDE GASPI_is_initialized
IRP_IF GASPI
use GASPI
integer(gaspi_return_t) :: res
integer(gaspi_rank_t) :: n
res = gaspi_proc_num(n)
GASPI_size = n
if (res /= GASPI_SUCCESS) then
print *, res
print *, 'Unable to get GASPI_size'
stop -1
endif
res = gaspi_proc_rank(n)
GASPI_rank = n
if (res /= GASPI_SUCCESS) then
print *, res
print *, 'Unable to get GASPI_rank'
stop -1
endif
is_GASPI_master = (GASPI_rank == 0)
IRP_ELSE
GASPI_rank = 0
GASPI_size = 1
is_GASPI_master = .True.
IRP_ENDIF
END_PROVIDER
subroutine gaspi_finalize()
implicit none
PROVIDE GASPI_is_initialized
IRP_IF GASPI
use GASPI
integer(gaspi_return_t) :: res
res = gaspi_proc_term(GASPI_BLOCK)
if (res /= GASPI_SUCCESS) then
print *, res
print *, 'Unable to finalize GASPI'
stop -1
endif
IRP_ENDIF
end subroutine

63
plugins/Hartree_Fock/DIIS.irp.f
View File

@ -94,7 +94,7 @@ END_PROVIDER
do i=1,AO_num
do j=1,AO_num
Xt(i,j) = X_Matrix_AO(j,i)
Xt(i,j) = S_half_inv(j,i)
enddo
enddo
@ -103,7 +103,7 @@ END_PROVIDER
call dgemm('N','N',AO_num,AO_num,AO_num, &
1.d0, &
Fock_matrix_AO,size(Fock_matrix_AO,1), &
X_Matrix_AO,size(X_Matrix_AO,1), &
S_half_inv,size(S_half_inv,1), &
0.d0, &
eigenvectors_Fock_matrix_AO,size(eigenvectors_Fock_matrix_AO,1))
@ -130,67 +130,10 @@ END_PROVIDER
call dgemm('N','N',AO_num,AO_num,AO_num, &
1.d0, &
X_matrix_AO,size(X_matrix_AO,1), &
S_half_inv,size(S_half_inv,1), &
scratch,size(scratch,1), &
0.d0, &
eigenvectors_Fock_matrix_AO,size(eigenvectors_Fock_matrix_AO,1))
END_PROVIDER
BEGIN_PROVIDER [ double precision, X_matrix_AO, (AO_num,AO_num) ]
BEGIN_DOC
! Matrix X = S^{-1/2} obtained by SVD
END_DOC
implicit none
integer :: num_linear_dependencies
integer :: LDA, LDC
double precision, allocatable :: U(:,:),Vt(:,:), D(:)
integer :: info, i, j, k
LDA = size(AO_overlap,1)
LDC = size(X_matrix_AO,1)
allocate( &
U(LDC,AO_num), &
Vt(LDA,AO_num), &
D(AO_num))
call svd( &
AO_overlap,LDA, &
U,LDC, &
D, &
Vt,LDA, &
AO_num,AO_num)
num_linear_dependencies = 0
do i=1,AO_num
print*,D(i)
if(abs(D(i)) <= threshold_overlap_AO_eigenvalues) then
D(i) = 0.d0
num_linear_dependencies += 1
else
ASSERT (D(i) > 0.d0)
D(i) = 1.d0/sqrt(D(i))
endif
do j=1,AO_num
X_matrix_AO(j,i) = 0.d0
enddo
enddo
write(*,*) 'linear dependencies',num_linear_dependencies
! stop
do k=1,AO_num
if(D(k) /= 0.d0) then
do j=1,AO_num
do i=1,AO_num
X_matrix_AO(i,j) = X_matrix_AO(i,j) + U(i,k)*D(k)*Vt(k,j)
enddo
enddo
endif
enddo
END_PROVIDER

8
plugins/Hartree_Fock/EZFIO.cfg
View File

@ -1,9 +1,3 @@
[threshold_overlap_ao_eigenvalues]
type: Threshold
doc: Threshold on the magnitude of the smallest eigenvalues of the overlap matrix in the AO basis
interface: ezfio,provider,ocaml
default: 1.e-6
[max_dim_diis]
type: integer
doc: Maximum size of the DIIS extrapolation procedure
@ -32,7 +26,7 @@ default: 500
type: Positive_float
doc: Energy shift on the virtual MOs to improve SCF convergence
interface: ezfio,provider,ocaml
default: 0.0
default: 0.1
[scf_algorithm]
type: character*(32)

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