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Add ezfio support

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This commit is contained in:
Thomas Applencourt 2015-04-03 14:12:51 +02:00
parent e5c2d5ee65
commit 37e049ea1a
6 changed files with 385 additions and 67 deletions
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183
scripts/pseudo/put_pseudo_in_ezfio.py Executable file
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@ -0,0 +1,183 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Create the pseudo potential for a given atom
Usage:
put_pseudo_in_ezfio.py --ezfio=<path> --atom=<atom>...
"""
import os
import sys
from docopt import docopt
from subprocess import Popen, PIPE
qpackage_root = os.environ['QPACKAGE_ROOT']
EZFIO = "{0}/EZFIO".format(qpackage_root)
sys.path = [EZFIO + "/Python"] + sys.path
from ezfio import ezfio
import re
p = re.compile(ur'\|(\d+)><\d+\|')
def get_pseudo_str(l_atom):
"""
Run EMSL_local for geting the str of the speudo potential
"""
EMSL_root = "{0}/EMSL_Basis/".format(qpackage_root)
EMSL_path = "{0}/EMSL_api.py".format(EMSL_root)
db_path = "{0}/db/Pseudo.db".format(EMSL_root)
l_cmd_atom = []
for a in l_atom:
l_cmd_atom += ["--atom", a]
l_cmd_head = [EMSL_path, "get_basis_data",
"--db_path", db_path,
"--basis", "BFD-Pseudo"]
process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE)
stdout, _ = process.communicate()
return stdout.strip()
def get_v_n_dz_local(str_ele):
"""
From a str_ele of the pseudo (aka only one ele in the str)
get the list ussefull for the Local potential : v_k n_k and dz_k
"""
l_v_k = []
l_n_k = []
l_dz_k = []
for l in str_ele.splitlines():
try:
v, n, dz = l.split()
v = float(v)
n = int(n)
dz = float(dz)
except ValueError:
pass
else:
l_v_k.append(v)
l_n_k.append(n)
l_dz_k.append(dz)
return l_v_k, l_n_k, l_dz_k
def get_v_n_dz_l_nonlocal(str_ele):
"""
From a str_ele of the pseudo (aka only one ele in the str)
get the list ussefull for the non Local potential
v_kl (v, l)
n_k (v, l)
dz_k (dz ,l)
"""
l_v_kl = []
l_n_kl = []
l_dz_kl = []
for l in str_ele.splitlines():
try:
v, n, dz, proj = l.split()
v = float(v)
n = int(n)
dz = float(dz)
l = int(p.match(proj).group(1))
except ValueError:
pass
else:
l_v_kl.append((v, l))
l_n_kl.append((n, l))
l_dz_kl.append((dz, l))
return l_v_kl, l_n_kl, l_dz_kl
if __name__ == "__main__":
arguments = docopt(__doc__)
# ___
# | ._ o _|_
# _|_ | | | |_
#
# ~#~#~#~#~ #
# E Z F I O #
# ~#~#~#~#~ #
ezfio_path = arguments["--ezfio"]
ezfio_path = os.path.expanduser(ezfio_path)
ezfio_path = os.path.expandvars(ezfio_path)
ezfio_path = os.path.abspath(ezfio_path)
ezfio.set_file("{0}".format(ezfio_path))
# ~#~#~#~#~#~#~#~#~#~#~ #
# P s e u d o _ d a t a #
# ~#~#~#~#~#~#~#~#~#~#~ #
l_ele = arguments["--atom"]
str_ = get_pseudo_str(l_ele)
# _
# |_) _. ._ _ _
# | (_| | _> (/_
#
l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ")
if str_ele]
for str_ele in l_str_ele:
# ~#~#~#~#~ #
# S p l i t #
# ~#~#~#~#~ #
l = str_ele.find("Local component:")
nl = str_ele.find("Non-local component")
# ~#~#~#~#~ #
# L o c a l #
# ~#~#~#~#~ #
print "local"
l_v, l_n, l_dz = get_v_n_dz_local(str_ele[l:nl])
print l_v
print l_n
print l_dz
ezfio.pseudo_klocmax = len(l_v)
ezfio.pseudo_v_k = l_v
ezfio.pseudo_n_k = l_n
ezfio.pseudo_dz_k = l_dz
# ~#~#~#~#~#~#~#~#~ #
# N o n _ L o c a l #
# ~#~#~#~#~#~#~#~#~ #
print "non local"
l_v_kl, l_n_kl, l_dz_kl = get_v_n_dz_l_nonlocal(str_ele[nl:])
print l_v_kl
print l_n_kl
print l_dz_kl
if l_v_kl:
ezfio.pseudo_lmax = max([i[1] for i in l_v_kl]) + 1
ezfio.pseudo_kmax = len(l_v_kl)
ezfio.pseudo_v_kl = l_v_kl
ezfio.pseudo_n_kl = l_n_kl
ezfio.pseudo_dz_kl = l_dz_kl

4
setup_environment.sh
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@ -17,7 +17,9 @@ export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P )
export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH}
export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts
export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts/pseudo
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml

1
src/Pseudo/NEEDED_MODULES
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@ -0,0 +1 @@
Ezfio_files Nuclei Output Utils

66
src/Pseudo/int.f90
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@ -1,60 +1,3 @@
!!
!! Computation of Vps, matrix element of the
!! pseudo-potential centered at point C
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! Vps= < Phi_A | Vloc(C) + Vpp(C) | Phi_B>
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! Phi_M (M=A,B) Cartesian gaussian orbital centered at point M :
!! Phi_M = (x-M_x)**n^M_x *(y-M_y)**n^M_y *(z-M_z)**n^M_z exp(-g_M rM**2)
!! with rM**2=(x-M_x)**2 + (y-M_y)**2 + (z-M_z)**2
!!
!!** Vloc(C)= \sum_{k=1}^klocmax v_k rC**n_k exp(-dz_k rC**2)
!!
!!** Vpp(C)= \sum_{l=0}^lmax v_l(rC) \sum_{m=-l}^{m=l} |Y_lm> <Y_lm|
!!
!! v_l(rC) = \sum_{k=1}^kmax v_kl rC**n_kl exp(-dz_kl rC**2)
!!
!! Y_lm : real spherical harmonics:
!! Y_00 = sqrt(1/4pi)
!! Y_11 = sqrt(3/4pi) xchap
!! Y_10 = sqrt(3/4pi) ychap
!! Y_1-1 = sqrt(3/4pi) zchap
!! Y_22 = sqrt(15/16pi) (xchap**2-ychap**2)
!! Y_21 = sqrt(15/4pi) xchap*zchap
!! Y_20 = sqrt(15/16pi)(-xchap**2-ychap**2+ 2 zchap**2)
!! Y_2-1 = sqrt(15/4pi) ychap*zchap
!! Y_2-2 = sqrt(15/4pi) xchap*ychap
!! etc.
!! xchap=x/r ychap=y/r zchap=z/r
!!
!! Routine computing <Phi_A|Vpp(C)|Phi_B> :
!! function Vpseudo(lmax,kmax,v_kl,n_kl,dz_kl,a,n_a,g_a,b,n_b,g_b,c)
!! lmax of formula above
!! kmax of formula above
!! v_kl = array v_kl(kmax_max,0:lmax_max)
!! n_kl = array n_kl(kmax_max,0:lmax_max)
!! dz_kl = array dz_kl(kmax_max,0:lmax_max)
!! n_a(1),n_a(2),n_a(3)
!! a(1),a(2),a(3)
!! g_a
!! n_b(1),n_b(2),n_b(3)
!! b(1),b(2),b(3)
!! g_b
!! c(1),c(2),c(3)
!!
!! Routine computing <Phi_A|Vloc(C)|Phi_B> :
!! function Vloc(klocmax,v_k,n_k,dz_k,a,n_a,g_a,b,n_b,g_b,c)
!! klocmax of formula above
!! v_k = array v_k(klocmax_max)
!! n_k = array n_k(klocmax_max)
!! dz_k= array dz_k(klocmax_max)
!! Routine total matrix element <Phi_A|Vloc(C)+Vlpp(C)|Phi_B> :
!! function Vps(a,n_a,g_a,b,n_b,g_b,c,klocmax,v_k,n_k,dz_k,lmax,kmax,v_kl,n_kl,dz_kl)
!!
!! Routines Vps_num, Vpseudo_num, and Vloc_num = brute force numerical
!! estimations of the same integrals
!! Vps= <Phi_A|Vloc(C)+Cpp(C)| Phi_B>
!!
!! with: Vloc(C)=\sum_{k=1}^klocmax v_k rC**n_k exp(-dz_k rC**2)
@ -1019,15 +962,6 @@ end
! Y_l^m(theta,phi) = i^(m+|m|) ([(2l+1)*(l-|m|)!]/[4pi*(l+|m|)!])^1/2
! P_l^|m|(cos(theta)) exp(i m phi)
double precision function fact(n)
implicit double precision(a-h,o-z)
fact=1.d0
if(n.eq.0)return
do i=1,n
fact=fact*dfloat(i)
enddo
end
subroutine erreur(x,n,rmoy,error)
implicit double precision(a-h,o-z)
dimension x(n)

10
src/Pseudo/pseudo.ezfio_config Normal file
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@ -0,0 +1,10 @@
pseudo
klocmax integer
v_k double precision (pseudo_klocmax)
n_k integer (pseudo_klocmax)
dz_k double precision (pseudo_klocmax)
lmax integer
kmax integer
v_kl double precision (pseudo_kmax,pseudo_lmax)
n_kl integer (pseudo_kmax,pseudo_lmax)
dz_kl double precision (pseudo_kmax,pseudo_lmax)

188
src/Pseudo/test_michel.irp.f Normal file
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@ -0,0 +1,188 @@
!!
!! Computation of Vps, matrix element of the
!! pseudo-potential centered at point C
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! Vps= < Phi_A | Vloc(C) + Vpp(C) | Phi_B>
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! Phi_M (M=A,B) Cartesian gaussian orbital centered at point M :
!! Phi_M = (x-M_x)**n^M_x *(y-M_y)**n^M_y *(z-M_z)**n^M_z exp(-g_M rM**2)
!! with rM**2=(x-M_x)**2 + (y-M_y)**2 + (z-M_z)**2
!!
!!** Vloc(C)= \sum_{k=1}^klocmax v_k rC**n_k exp(-dz_k rC**2)
!!
!!** Vpp(C)= \sum_{l=0}^lmax v_l(rC) \sum_{m=-l}^{m=l} |Y_lm> <Y_lm|
!!
!! v_l(rC) = \sum_{k=1}^kmax v_kl rC**n_kl exp(-dz_kl rC**2)
!!
!! Y_lm : real spherical harmonics:
!! Y_00 = sqrt(1/4pi)
!! Y_11 = sqrt(3/4pi) xchap
!! Y_10 = sqrt(3/4pi) ychap
!! Y_1-1 = sqrt(3/4pi) zchap
!! Y_22 = sqrt(15/16pi) (xchap**2-ychap**2)
!! Y_21 = sqrt(15/4pi) xchap*zchap
!! Y_20 = sqrt(15/16pi)(-xchap**2-ychap**2+ 2 zchap**2)
!! Y_2-1 = sqrt(15/4pi) ychap*zchap
!! Y_2-2 = sqrt(15/4pi) xchap*ychap
!! etc.
!! xchap=x/r ychap=y/r zchap=z/r
!!
!! Routine computing <Phi_A|Vpp(C)|Phi_B> :
!! function Vpseudo(lmax,kmax,v_kl,n_kl,dz_kl,a,n_a,g_a,b,n_b,g_b,c)
!! lmax of formula above
!! kmax of formula above
!! v_kl = array v_kl(kmax_max,0:lmax_max)
!! n_kl = array n_kl(kmax_max,0:lmax_max)
!! dz_kl = array dz_kl(kmax_max,0:lmax_max)
!! n_a(1),n_a(2),n_a(3)
!! a(1),a(2),a(3)
!! g_a
!! n_b(1),n_b(2),n_b(3)
!! b(1),b(2),b(3)
!! g_b
!! c(1),c(2),c(3)
!!
!! Routine computing <Phi_A|Vloc(C)|Phi_B> :
!! function Vloc(klocmax,v_k,n_k,dz_k,a,n_a,g_a,b,n_b,g_b,c)
!! klocmax of formula above
!! v_k = array v_k(klocmax_max)
!! n_k = array n_k(klocmax_max)
!! dz_k= array dz_k(klocmax_max)
!! Routine total matrix element <Phi_A|Vloc(C)+Vlpp(C)|Phi_B> :
!! function Vps(a,n_a,g_a,b,n_b,g_b,c,klocmax,v_k,n_k,dz_k,lmax,kmax,v_kl,n_kl,dz_kl)
!!
!! Routines Vps_num, Vpseudo_num, and Vloc_num = brute force numerical
!! estimations of the same integrals
program compute_integrals_pseudo
implicit none
integer n_a(3),n_b(3),npts
double precision g_a,g_b,a(3),b(3),c(3)
double precision Vpseudo,Vpseudo_num,Vloc,Vloc_num
double precision v3,v4
double precision vps,vps_num
! PSEUDOS
integer nptsgridmax,nptsgrid
double precision coefs_pseudo,ptsgrid
double precision rmax
double precision time_1,time_2,time_3,time_4,time_5
integer kga,kgb,na1,na2,na3,nb1,nb2,nb3
CALL RANDOM_SEED()
nptsgrid=50
call initpseudos(nptsgrid)
PROVIDE ezfio_filename
!
! | _ _ _. |
! |_ (_) (_ (_| |
!
integer klocmax
integer, allocatable :: n_k(:)
double precision, allocatable :: v_k(:), dz_k(:)
call ezfio_get_pseudo_klocmax(klocmax)
allocate(n_k(klocmax),v_k(klocmax), dz_k(klocmax))
call ezfio_get_pseudo_v_k(v_k)
call ezfio_get_pseudo_n_k(n_k)
call ezfio_get_pseudo_dz_k(dz_k)
print*, "klocmax", klocmax
print*, "n_k_ezfio", n_k
print*, "v_k_ezfio",v_k
print*, "dz_k_ezfio", dz_k
!
! |\ | _ ._ | _ _ _. |
! | \| (_) | | | (_) (_ (_| |
!
!! Parameters of non local part of pseudo:
integer :: kmax,lmax
integer, allocatable :: n_kl(:,:)
double precision, allocatable :: v_kl(:,:), dz_kl(:,:)
call ezfio_get_pseudo_lmax(lmax)
call ezfio_get_pseudo_kmax(kmax)
lmax = lmax - 1
allocate(n_kl(kmax,0:lmax), v_kl(kmax,0:lmax), dz_kl(kmax,0:lmax))
call ezfio_get_pseudo_n_kl(n_kl)
call ezfio_get_pseudo_v_kl(v_kl)
call ezfio_get_pseudo_dz_kl(dz_kl)
print*, "lmax",lmax
print*, "kmax", kmax
print*,"n_kl_ezfio", n_kl
print*,"v_kl_ezfio", v_kl
print*,"dz_kl_ezfio", dz_kl
! _
! / _. | _ |
! \_ (_| | (_ |_| |
!
write(*,*)'a?'
read*,a(1),a(2),a(3)
!write(*,*)'b?'
!read*,b(1),b(2),b(3)
b(1)=-0.1d0
b(2)=-0.2d0
b(3)=0.3d0
!write(*,*)'a?'
!read*,c(1),c(2),c(3)
c(1)=0.1d0
c(2)=0.2d0
c(3)=0.3d0
print*,'ntps? rmax for brute force integration'
read*,npts,rmax
do kga=0,5
g_a=10.d0**kga
do kgb=0,5
g_b=10.d0**kgb
do na1=0,1
do na2=0,1
do na3=0,1
do nb1=0,1
do nb2=0,1
do nb3=0,1
n_a(1)=na1
n_a(2)=na2
n_a(3)=na3
n_b(1)=nb1
n_b(2)=nb2
n_b(3)=nb3
v3=Vps(a,n_a,g_a,b,n_b,g_b,c,klocmax,v_k,n_k,dz_k,lmax,kmax,v_kl,n_kl,dz_kl)
v4=Vps_num(npts,rmax,a,n_a,g_a,b,n_b,g_b,c,klocmax,v_k,n_k,dz_k,lmax,kmax,v_kl,n_kl,dz_kl)
print*,'Vps= ',v3,' Vps_num=',v4,' diff=',v4-v3
write(33,'(3f10.6)')v3,v4,v4-v3
enddo
enddo
enddo
enddo
enddo
enddo
enddo
enddo
end