mirror of
https://github.com/LCPQ/quantum_package
synced 2024-12-22 20:35:19 +01:00
Merge branch 'master' of github.com:TApplencourt/quantum_package
This commit is contained in:
TApplencourt
commit
b521a8d015
118
data/list_element.txt
Normal file
118
data/list_element.txt
Normal file
@ -0,0 +1,118 @@
|
||||
1 H Hydrogen
|
||||
2 He Helium
|
||||
3 Li Lithium
|
||||
4 Be Beryllium
|
||||
5 B Boron
|
||||
6 C Carbon
|
||||
7 N Nitrogen
|
||||
8 O Oxygen
|
||||
9 F Fluorine
|
||||
10 Ne Neon
|
||||
11 Na Sodium
|
||||
12 Mg Magnesium
|
||||
13 Al Aluminum
|
||||
14 Si Silicon
|
||||
15 P Phosphorus
|
||||
16 S Sulfur
|
||||
17 Cl Chlorine
|
||||
18 Ar Argon
|
||||
19 K Potassium
|
||||
20 Ca Calcium
|
||||
21 Sc Scandium
|
||||
22 Ti Titanium
|
||||
23 V Vanadium
|
||||
24 Cr Chromium
|
||||
25 Mn Manganese
|
||||
26 Fe Iron
|
||||
27 Co Cobalt
|
||||
28 Ni Nickel
|
||||
29 Cu Copper
|
||||
30 Zn Zinc
|
||||
31 Ga Gallium
|
||||
32 Ge Germanium
|
||||
33 As Arsenic
|
||||
34 Se Selenium
|
||||
35 Br Bromine
|
||||
36 Kr Krypton
|
||||
37 Rb Rubidium
|
||||
38 Sr Strontium
|
||||
39 Y Yttrium
|
||||
40 Zr Zirconium
|
||||
41 Nb Niobium
|
||||
42 Mo Molybdenum
|
||||
43 Tc Technetium
|
||||
44 Ru Ruthenium
|
||||
45 Rh Rhodium
|
||||
46 Pd Palladium
|
||||
47 Ag Silver
|
||||
48 Cd Cadmium
|
||||
49 In Indium
|
||||
50 Sn Tin
|
||||
51 Sb Antimony
|
||||
52 Te Tellurium
|
||||
53 I Iodine
|
||||
54 Xe Xenon
|
||||
55 Cs Cesium
|
||||
56 Ba Barium
|
||||
57 La Lanthanum
|
||||
58 Ce Cerium
|
||||
59 Pr Praseodymium
|
||||
60 Nd Neodymium
|
||||
61 Pm Promethium
|
||||
62 Sm Samarium
|
||||
63 Eu Europium
|
||||
64 Gd Gadolinium
|
||||
65 Tb Terbium
|
||||
66 Dy Dysprosium
|
||||
67 Ho Holmium
|
||||
68 Er Erbium
|
||||
69 Tm Thulium
|
||||
70 Yb Ytterbium
|
||||
71 Lu Lutetium
|
||||
72 Hf Hafnium
|
||||
73 Ta Tantalum
|
||||
74 W Tungsten
|
||||
75 Re Rhenium
|
||||
76 Os Osmium
|
||||
77 Ir Iridium
|
||||
78 Pt Platinum
|
||||
79 Au Gold
|
||||
80 Hg Mercury
|
||||
81 Tl Thallium
|
||||
82 Pb Lead
|
||||
83 Bi Bismuth
|
||||
84 Po Polonium
|
||||
85 At Astatine
|
||||
86 Rn Radon
|
||||
87 Fr Francium
|
||||
88 Ra Radium
|
||||
89 Ac Actinium
|
||||
90 Th Thorium
|
||||
91 Pa Protactinium
|
||||
92 U Uranium
|
||||
93 Np Neptunium
|
||||
94 Pu Plutonium
|
||||
95 Am Americium
|
||||
96 Cm Curium
|
||||
97 Bk Berkelium
|
||||
98 Cf Californium
|
||||
99 Es Einsteinium
|
||||
100 Fm Fermium
|
||||
101 Md Mendelevium
|
||||
102 No Nobelium
|
||||
103 Lr Lawrencium
|
||||
104 Rf Rutherfordium
|
||||
105 Db Dubnium
|
||||
106 Sg Seaborgium
|
||||
107 Bh Bohrium
|
||||
108 Hs Hassium
|
||||
109 Mt Meitnerium
|
||||
110 Ds Darmstadtium
|
||||
111 Rg Roentgenium
|
||||
112 Cn Copernicium
|
||||
113 Uut Ununtrium
|
||||
114 Fl Flerovium
|
||||
115 Uup Ununpentium
|
||||
116 Lv Livermorium
|
||||
117 Uus Ununseptium
|
||||
118 Uuo Ununoctium
|
||||
@ -11,7 +11,8 @@ module Determinants_by_hand : sig
|
||||
psi_coef : Det_coef.t array;
|
||||
psi_det : Determinant.t array;
|
||||
} with sexp
|
||||
val read : unit -> t option
|
||||
val read : unit -> t
|
||||
val read_maybe : unit -> t option
|
||||
val write : t -> unit
|
||||
val to_string : t -> string
|
||||
val to_rst : t -> Rst_string.t
|
||||
@ -210,13 +211,6 @@ end = struct
|
||||
|
||||
let read () =
|
||||
if (Ezfio.has_mo_basis_mo_tot_num ()) then
|
||||
let n_det =
|
||||
read_n_det ()
|
||||
in
|
||||
if ( (Det_number.to_int n_det) > n_det_read_max ) then
|
||||
None
|
||||
else
|
||||
Some
|
||||
{ n_int = read_n_int () ;
|
||||
bit_kind = read_bit_kind () ;
|
||||
n_det = read_n_det () ;
|
||||
@ -224,6 +218,17 @@ end = struct
|
||||
psi_coef = read_psi_coef () ;
|
||||
psi_det = read_psi_det () ;
|
||||
}
|
||||
else
|
||||
failwith "No molecular orbitals, so no determinants"
|
||||
;;
|
||||
|
||||
let read_maybe () =
|
||||
let n_det =
|
||||
read_n_det ()
|
||||
in
|
||||
if ( (Det_number.to_int n_det) < n_det_read_max ) then
|
||||
try Some (read ()) with
|
||||
| Failure _ -> None
|
||||
else
|
||||
None
|
||||
;;
|
||||
|
||||
@ -36,7 +36,7 @@ let bind_socket ~socket_type ~socket ~address =
|
||||
| 0 -> failwith @@ Printf.sprintf
|
||||
"Unable to bind the %s socket : %s "
|
||||
socket_type address
|
||||
| -1 -> ();
|
||||
| -1 -> ()
|
||||
| i ->
|
||||
try
|
||||
ZMQ.Socket.bind socket address;
|
||||
|
||||
@ -43,9 +43,7 @@ let psi_det () =
|
||||
failwith "Error reading EZFIO file";
|
||||
Ezfio.set_file ezfio_filename;
|
||||
let psi_det =
|
||||
match Input.Determinants_by_hand.read () with
|
||||
| Some psi_det -> psi_det
|
||||
| _ -> failwith "Error reading the mo set"
|
||||
Input.Determinants_by_hand.read ()
|
||||
in
|
||||
Input.Determinants_by_hand.to_rst psi_det
|
||||
|> Rst_string.to_string
|
||||
@ -56,5 +54,5 @@ let psi_det () =
|
||||
let () =
|
||||
basis ();
|
||||
mo ();
|
||||
psi_det ();
|
||||
psi_det ()
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
open Core.Std
|
||||
|
||||
let () =
|
||||
Message.of_string "new_job tcp://127.0.0.1 inproc://ao_ints:12345 ao_integrals"
|
||||
Message.of_string "new_job ao_integrals tcp://127.0.0.1 inproc://ao_ints:12345"
|
||||
|> Message.to_string
|
||||
|> print_endline
|
||||
;
|
||||
@ -37,7 +37,7 @@ let () =
|
||||
;
|
||||
|
||||
try
|
||||
Message.of_string "new_job inproc://ao_ints tcp://127.0.0.1:12345 ao_integrals"
|
||||
Message.of_string "new_job ao_integrals inproc://ao_ints tcp://127.0.0.1:12345"
|
||||
|> Message.to_string
|
||||
|> print_endline
|
||||
;
|
||||
|
||||
@ -9,6 +9,7 @@ print "#QP -> QMCPACK"
|
||||
|
||||
from ezfio import ezfio
|
||||
|
||||
import os
|
||||
import sys
|
||||
ezfio_path = sys.argv[1]
|
||||
|
||||
@ -17,7 +18,15 @@ ezfio.set_file(ezfio_path)
|
||||
do_pseudo = ezfio.get_pseudo_do_pseudo()
|
||||
if do_pseudo:
|
||||
print "do_pseudo True"
|
||||
print "The charge of nucl will be decreasced for taking into acount the pseudo potentiel"
|
||||
from qp_path import QP_ROOT
|
||||
|
||||
l_ele_path = os.path.join(QP_ROOT,"data","list_element.txt")
|
||||
with open(l_ele_path, "r") as f:
|
||||
data_raw = f.read()
|
||||
|
||||
l_element_raw = data_raw.split("\n")
|
||||
l_element = [element_raw.split() for element_raw in l_element_raw]
|
||||
d_z = dict((abr, z) for (z, abr, ele) in l_element)
|
||||
else:
|
||||
print "do_pseudo False"
|
||||
|
||||
@ -68,7 +77,10 @@ print "nucl_num", len(l_label)
|
||||
print "Atomic coord in Bohr"
|
||||
|
||||
for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
|
||||
print list_to_string(t)
|
||||
t_1 = d_z[t[0]] if do_pseudo else t[1]
|
||||
|
||||
t_new = [t[0],t_1,t[2]]
|
||||
print list_to_string(t_new)
|
||||
|
||||
#
|
||||
# Call externet process to get the sysmetry
|
||||
@ -79,7 +91,6 @@ process = subprocess.Popen(
|
||||
stdout=subprocess.PIPE)
|
||||
out, err = process.communicate()
|
||||
|
||||
print len(out.split("\n\n\n"))
|
||||
basis_raw, sym_raw, _ , det_raw, _ = out.split("\n\n\n")
|
||||
|
||||
# _ __
|
||||
@ -310,8 +321,8 @@ if do_pseudo:
|
||||
if l_dump:
|
||||
l_str.append(l_dump)
|
||||
|
||||
str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE -1 AND LMAX {2} ARE"
|
||||
print str_.format(a, i + 1, int(len(l_str) - 1))
|
||||
str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
|
||||
print str_.format(a, i + 1, int(d_z[a])-int(l_charge[i]), int(len(l_str) - 1))
|
||||
|
||||
for i, l in enumerate(l_str):
|
||||
str_ = "FOR L= {0} COEFF N ZETA"
|
||||
@ -319,7 +330,8 @@ if do_pseudo:
|
||||
for ii, ll in enumerate(l):
|
||||
print " ", ii + 1, ll
|
||||
|
||||
str_ = "THE ECP RUN REMOVES -1 CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
|
||||
str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
|
||||
print str_.format(sum([int(d_z[a])-int(l_charge[i]) for i,a in enumerate(l_label)]))
|
||||
print "END_PSEUDO"
|
||||
|
||||
# _
|
||||
|
||||
@ -14,6 +14,12 @@ program qmcpack
|
||||
enddo
|
||||
enddo
|
||||
call ezfio_set_ao_basis_ao_coef(ao_coef)
|
||||
do j=1,mo_tot_num
|
||||
do i=1,ao_num
|
||||
mo_coef(i,j) *= 1.d0/ao_coef_normalization_factor(i)
|
||||
enddo
|
||||
enddo
|
||||
call save_mos
|
||||
call system('rm '//trim(ezfio_filename)//'/mo_basis/ao_md5')
|
||||
call system('$QP_ROOT/src/qmcpack/qp_convert_qmcpack_to_ezfio.py '//trim(ezfio_filename))
|
||||
|
||||
|
||||
@ -75,7 +75,7 @@ let get s =
|
||||
| Ao_basis ->
|
||||
f Ao_basis.(read, to_rst)
|
||||
| Determinants_by_hand ->
|
||||
f Determinants_by_hand.(read, to_rst)
|
||||
f Determinants_by_hand.(read_maybe, to_rst)
|
||||
{section_to_rst}
|
||||
end
|
||||
with
|
||||
|
||||
@ -52,9 +52,6 @@ END_PROVIDER
|
||||
enddo
|
||||
enddo
|
||||
ao_coef_normalization_factor(i) = 1.d0/sqrt(norm)
|
||||
do j=1,ao_prim_num(i)
|
||||
ao_coef_normalized(i,j) = ao_coef_normalized(i,j) * ao_coef_normalization_factor(i)
|
||||
enddo
|
||||
enddo
|
||||
|
||||
END_PROVIDER
|
||||
|
||||
Loading…
Reference in New Issue
Block a user