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mirror of https://github.com/QuantumPackage/qp2.git synced 2024-07-20 17:53:25 +02:00

Merge branch 'dev-stable' of github.com:QuantumPackage/qp2 into dev-stable

This commit is contained in:
Anthony Scemama 2023-10-26 15:06:57 +02:00
commit bae76e9243
21 changed files with 214 additions and 28 deletions

4
bin/python Executable file
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@ -0,0 +1,4 @@
#!/bin/bash
exec python3 $@

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@ -1,6 +1,7 @@
#!/bin/bash
export QP_ROOT=$(dirname "$(readlink -f "$0")")/..
REALPATH=$( cd "$(dirname "$0")" ; pwd -P )
export QP_ROOT=${REALPATH}/..
bash --init-file <(cat << EOF
[[ -f /etc/bashrc ]] && source /etc/bashrc

22
bin/zcat Executable file
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@ -0,0 +1,22 @@
#!/bin/bash
# On Darwin: try gzcat if available, otherwise use Python
if [[ $(uname -s) = Darwin ]] ; then
which gzcat &> /dev/null
if [[ $? -eq 0 ]] ; then
exec gzcat $@
else
exec python3 << EOF
import sys
import gzip
with gzip.open("$1", "rt") as f:
print(f.read())
EOF
fi
else
command=$(which -a zcat | grep -v 'qp2/bin/' | head -1)
exec $command $@
fi

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@ -10,7 +10,7 @@
#
#
[COMMON]
FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

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@ -13,7 +13,7 @@
#
#
[COMMON]
FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
LAPACK_LIB : -larmpl_lp64_mp
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

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@ -10,7 +10,7 @@
#
#
[COMMON]
FC : gfortran -ffree-line-length-none -I . -mavx -g -fPIC
FC : gfortran -ffree-line-length-none -I . -mavx -g -fPIC -std=legacy
LAPACK_LIB : -llapack -lblas
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED

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@ -10,7 +10,7 @@
#
#
[COMMON]
FC : gfortran -g -ffree-line-length-none -I . -fPIC
FC : gfortran -g -ffree-line-length-none -I . -fPIC -std=legacy
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

62
config/gfortran_macos.cfg Normal file
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@ -0,0 +1,62 @@
# Common flags
##############
#
# -ffree-line-length-none : Needed for IRPF90 which produces long lines
# -lblas -llapack : Link with libblas and liblapack libraries provided by the system
# -I . : Include the curent directory (Mandatory)
#
# --ninja : Allow the utilisation of ninja. (Mandatory)
# --align=32 : Align all provided arrays on a 32-byte boundary
#
#
[COMMON]
FC : gfortran -ffree-line-length-none -I . -g -fPIC -std=legacy
LAPACK_LIB : -llapack -lblas
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED -DMACOS
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -Ofast : Disregard strict standards compliance. Enables all -O3 optimizations.
# It also enables optimizations that are not valid
# for all standard-compliant programs. It turns on
# -ffast-math and the Fortran-specific
# -fno-protect-parens and -fstack-arrays.
[OPT]
FCFLAGS : -Ofast -march=native
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -Ofast
# Debugging flags
#################
#
# -fcheck=all : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
#
[DEBUG]
FCFLAGS : -fcheck=all -g
# OpenMP flags
#################
#
[OPENMP]
FC : -fopenmp
IRPF90_FLAGS : --openmp

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@ -10,7 +10,7 @@
#
#
[COMMON]
FC : mpif90 -ffree-line-length-none -I . -g -fPIC
FC : mpif90 -ffree-line-length-none -I . -g -fPIC -std=legacy
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI -DSET_NESTED

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@ -10,7 +10,7 @@
#
#
[COMMON]
FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
FC : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
LAPACK_LIB : -lopenblas
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

7
configure vendored
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@ -19,7 +19,11 @@ git submodule init
git submodule update
# Update ARM or x86 dependencies
ARCHITECTURE=$(uname -m)
SYSTEM=$(uname -s)
if [[ $SYSTEM = "Linux" ]] ; then
SYSTEM=""
fi
ARCHITECTURE=$(uname -m)$SYSTEM
cd ${QP_ROOT}/external/qp2-dependencies
git checkout master
git pull
@ -275,6 +279,7 @@ EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file qp2-dependencies/zeromq-4.2.5.tar.gz
cd zeromq-*
[[ "${SYSTEM}" = "Darwin" ]] && ./autogen.sh
./configure --prefix="\$QP_ROOT" --without-libsodium --enable-libunwind=no
make -j 8
make install

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@ -11,7 +11,11 @@ fi
cd ${QP_ROOT}/data
rm -f executables
if [[ "$(uname -s)" = "Darwin" ]] ; then
EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -perm +111 -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort )
else
EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -executable -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort )
fi
for EXE in $EXES
do

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@ -53,7 +53,6 @@ function run {
@test "B-B" {
qp set_file b2_stretched.ezfio
run b2_stretched.zmt 1 0 6-31g
}

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@ -33,6 +33,8 @@ BEGIN_PROVIDER [ character*(1024), ezfio_filename ]
call ezfio_set_file(ezfio_filename)
IRP_IF MACOS
IRP_ELSE
! Adjust out-of-memory killer flag such that the current process will be
! killed first by the OOM killer, allowing compute nodes to survive
integer :: getpid
@ -40,6 +42,7 @@ BEGIN_PROVIDER [ character*(1024), ezfio_filename ]
write(pidc,*) getpid()
write(command,*) 'echo 15 > /proc//'//trim(adjustl(pidc))//'/oom_adj'
call system(command)
IRP_ENDIF
PROVIDE file_lock

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@ -39,7 +39,7 @@ rm -rf $EZFIO
qp create_ezfio -b def2-svp hcn.xyz -o $EZFIO
qp run scf
mv hcn_charges.xyz ${EZFIO}_point_charges.xyz
python write_pt_charges.py ${EZFIO}
python3 write_pt_charges.py ${EZFIO}
qp set nuclei point_charges True
qp run scf | tee ${EZFIO}.pt_charges.out
energy="$(ezfio get hartree_fock energy)"

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@ -99,6 +99,7 @@ subroutine grad1_j12_mu(r1, r2, grad)
stop
endif
grad = -grad
return
end subroutine grad1_j12_mu
@ -486,6 +487,13 @@ subroutine mu_r_val_and_grad(r1, r2, mu_val, mu_der)
!!!!!!!!! rho1,rho2,rho1+rho2
call get_all_rho_grad_rho(r1,r2,rho1,rho2,grad_rho1)
rho_tot = rho1 + rho2
! if(rho_tot.lt.1.d-10)rho_tot = 1.d-10
if(rho_tot.lt.1.d-10)then
mu_val = mu_erf
mu_der = 0.d0
return
endif
if(rho_tot.lt.1.d-10)rho_tot = 1.d-10
inv_rho_tot = 1.d0/rho_tot
! f(rho) = mu_r_ct * rho**beta_rho_power + mu_erf
@ -506,18 +514,26 @@ subroutine mu_r_val_and_grad(r1, r2, mu_val, mu_der)
! d/dx1 f[rho(r1)] = [0.5 alpha / sqrt(rho(r1)) ] (d rho(r1) / dx1)
!
! d/dx1 (rho(r1) f[rho(r1)] = rho(r1) * d/dx1 f[rho(r1)] + f[rho(r1)] * d/dx1 rho(r1)
!!!!!!!!! rho1,rho2,rho1+rho2
call get_all_rho_grad_rho(r1,r2,rho1,rho2,grad_rho1)
rho_tot = rho1 + rho2
! if(rho_tot.lt.1.d-10)rho_tot = 1.d-10
if(rho_tot.lt.1.d-10)then
mu_val = mu_erf
mu_der = 0.d0
return
endif
if(rho_tot.lt.1.d-10)rho_tot = 1.d-10
inv_rho_tot = 1.d0/rho_tot
! f(rho) = mu_r_ct * rho**beta_rho_power + mu_erf
call get_all_f_rho_simple(rho1,rho2,mu_r_ct,mu_erf,beta_rho_power,f_rho1,d_drho_f_rho1,f_rho2)
! f(rho) = (mu_r_ct* rho)**beta_rho_power * erf(zeta_erf_mu_of_r * rho) + mu_eff * (1 - erf(zeta_erf_mu_of_r*rho))
call get_all_f_rho_erf(rho1,rho2,mu_r_ct,beta_rho_power,mu_erf,zeta_erf_mu_of_r,f_rho1,d_drho_f_rho1,f_rho2)
d_dx1_f_rho1(1:3) = d_drho_f_rho1 * grad_rho1(1:3)
d_dx_rho_f_rho(1:3) = rho1 * d_dx1_f_rho1(1:3) + f_rho1 * grad_rho1(1:3)
mu_val = 0.5d0 * ( f_rho1 + f_rho2)
mu_der(1:3) = d_dx_rho_f_rho(1:3)
nume = rho1 * f_rho1 + rho2 * f_rho2
mu_val = nume * inv_rho_tot
mu_der(1:3) = inv_rho_tot*inv_rho_tot * (rho_tot * d_dx_rho_f_rho(1:3) - grad_rho1(1:3) * nume)
else
print *, ' j1b_type = ', j1b_type, 'not implemented yet'
stop
@ -676,8 +692,17 @@ subroutine get_all_f_rho_simple(rho1,rho2,alpha,mu0,beta,f_rho1,d_drho_f_rho1,f_
double precision, intent(in) :: rho1,rho2,alpha,mu0,beta
double precision, intent(out):: f_rho1,d_drho_f_rho1,f_rho2
double precision :: tmp
call f_mu_and_deriv_mu_simple(rho1,alpha,mu0,beta,f_rho1,d_drho_f_rho1)
call f_mu_and_deriv_mu_simple(rho2,alpha,mu0,beta,f_rho2,tmp)
if(rho1.lt.1.d-10)then
f_rho1 = 0.d0
d_drho_f_rho1 = 0.d0
else
call f_mu_and_deriv_mu_simple(rho1,alpha,mu0,beta,f_rho1,d_drho_f_rho1)
endif
if(rho2.lt.1.d-10)then
f_rho2 = 0.d0
else
call f_mu_and_deriv_mu_simple(rho2,alpha,mu0,beta,f_rho2,tmp)
endif
end
subroutine f_mu_and_deriv_mu_simple(rho,alpha,mu0,beta,f_mu,d_drho_f_mu)
@ -691,10 +716,53 @@ subroutine f_mu_and_deriv_mu_simple(rho,alpha,mu0,beta,f_mu,d_drho_f_mu)
END_DOC
double precision, intent(in) :: rho,alpha,mu0,beta
double precision, intent(out) :: f_mu,d_drho_f_mu
f_mu = alpha * (rho)**beta + mu0
d_drho_f_mu = alpha * beta * rho**(beta-1.d0)
f_mu = alpha**beta * (rho)**beta + mu0
d_drho_f_mu = alpha**beta * beta * rho**(beta-1.d0)
end
! ---
subroutine f_mu_and_deriv_mu_erf(rho,alpha,zeta,mu0,beta,f_mu,d_drho_f_mu)
implicit none
include 'constants.include.F'
BEGIN_DOC
! function giving mu as a function of rho
!
! f_mu = (alpha * rho)**zeta * erf(beta * rho) + mu0 * (1 - erf(beta*rho))
!
! and its derivative with respect to rho d_drho_f_mu
!
! d_drho_f_mu = 2 beta/sqrt(pi) * exp(-(beta*rho)**2) * ( (alpha*rho)**zeta - mu0)
! + alpha * zeta * (alpha *rho)**(zeta-1) * erf(beta*rho)
END_DOC
double precision, intent(in) :: rho,alpha,mu0,beta,zeta
double precision, intent(out) :: f_mu,d_drho_f_mu
f_mu = (alpha * rho)**zeta * derf(beta * rho) + mu0 * (1.d0 - derf(beta*rho))
d_drho_f_mu = 2.d0 * beta * inv_sq_pi * dexp(-(beta*rho)**2) * ( (alpha*rho)**zeta - mu0) &
+ alpha * zeta * (alpha *rho)**(zeta-1) * derf(beta*rho)
end
subroutine get_all_f_rho_erf(rho1,rho2,alpha,zeta,mu0,beta,f_rho1,d_drho_f_rho1,f_rho2)
implicit none
BEGIN_DOC
! returns the values f(mu(r1)), f(mu(r2)) and d/drho(1) f(mu(r1))
! with f_mu = (alpha * rho)**zeta * erf(beta * rho) + mu0 * (1 - erf(beta*rho))
END_DOC
double precision, intent(in) :: rho1,rho2,alpha,mu0,beta,zeta
double precision, intent(out):: f_rho1,d_drho_f_rho1,f_rho2
double precision :: tmp
if(rho1.lt.1.d-10)then
f_rho1 = mu_erf
d_drho_f_rho1 = 0.d0
else
call f_mu_and_deriv_mu_erf(rho1,alpha,zeta,mu0,beta,f_rho1,d_drho_f_rho1)
endif
if(rho2.lt.1.d-10)then
f_rho2 = mu_erf
else
call f_mu_and_deriv_mu_erf(rho2,alpha,zeta,mu0,beta,f_rho2,tmp)
endif
end

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@ -13,9 +13,9 @@ subroutine routine_print
integer :: i_unit_output,getUnitAndOpen
output=trim(ezfio_filename)//'.mu_of_r'
i_unit_output = getUnitAndOpen(output,'w')
integer :: ipoint,nx
double precision :: xmax,xmin,r(3),dx
double precision :: mu_val, mu_der(3),dm_a,dm_b,grad
integer :: ipoint,nx,i
double precision :: xmax,xmin,r(3),dx,sigma
double precision :: mu_val, mu_der(3),dm_a,dm_b,grad,grad_dm_a(3), grad_dm_b(3)
xmax = 5.D0
xmin = -5.D0
nx = 10000
@ -24,10 +24,15 @@ subroutine routine_print
r(1) = xmin
do ipoint = 1, nx
call mu_r_val_and_grad(r, r, mu_val, mu_der)
call dm_dft_alpha_beta_at_r(r,dm_a,dm_b)
call density_and_grad_alpha_beta(r,dm_a,dm_b, grad_dm_a, grad_dm_b)
sigma = 0.d0
do i = 1,3
sigma += grad_dm_a(i)**2
enddo
sigma=dsqrt(sigma)
grad = mu_der(1)**2 + mu_der(2)**2 + mu_der(3)**2
grad = dsqrt(grad)
write(i_unit_output,'(100(F16.7,X))')r(1),mu_val,dm_a+dm_b,grad
write(i_unit_output,'(100(F16.7,X))')r(1),mu_val,dm_a+dm_b,grad,sigma/dm_a
r(1) += dx
enddo
end

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@ -52,7 +52,7 @@ fncharges.write(" "+str(n_charges)+'\n')
fncharges.close()
mv_in_ezfio(EZFIO,tmp)
# Write the file containing the charges and set in EZFIO folder
# Write the file containing the charges and set in EZFIO folder
tmp="pts_charge_z"
fcharges = open(tmp,'w')
fcharges.write(" 1\n")

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@ -158,13 +158,19 @@ default: 0
type: double precision
doc: a parameter used to define mu(r)
interface: ezfio, provider, ocaml
default: 6.203504908994001e-1
default: 1.5
[beta_rho_power]
type: double precision
doc: a parameter used to define mu(r)
interface: ezfio, provider, ocaml
default: 0.5
default: 0.33333
[zeta_erf_mu_of_r]
type: double precision
doc: a parameter used to define mu(r)
interface: ezfio, provider, ocaml
default: 1.
[thr_degen_tc]
type: Threshold

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@ -13,7 +13,7 @@ subroutine routine
output=trim(ezfio_filename)//'.wf_sorted'
i_unit_output = getUnitAndOpen(output,'w')
do i= 1, N_det
write(i_unit_output,*)i,dabs(psi_coef_sorted(i,1))
write(i_unit_output,*)i,dabs(psi_coef_sorted(i,1)),dabs(psi_coef_sorted(i,1)/psi_coef_sorted(1,1))
enddo
end

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@ -33,6 +33,8 @@ subroutine resident_memory(value)
call usleep(10)
value = 0.d0
IRP_IF MACOS
IRP_ELSE
iunit = getUnitAndOpen('/proc/self/status','r')
do
read(iunit,*,err=10,end=20) key, value
@ -43,6 +45,7 @@ subroutine resident_memory(value)
end do
20 continue
close(iunit)
IRP_ENDIF
value = value / (1024.d0*1024.d0)
call unlock_io()
end function
@ -58,6 +61,9 @@ subroutine total_memory(value)
double precision, intent(out) :: value
call lock_io()
value = 0.d0
IRP_IF MACOS
IRP_ELSE
iunit = getUnitAndOpen('/proc/self/status','r')
do
read(iunit,*,err=10,end=20) key, value
@ -68,6 +74,7 @@ subroutine total_memory(value)
end do
20 continue
close(iunit)
IRP_ENDIF
value = value / (1024.d0*1024.d0)
call unlock_io()
end function