mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-08-25 13:41:47 +02:00
Merge branch 'dev-stable' of github.com:QuantumPackage/qp2 into dev-stable
This commit is contained in:
commit
bae76e9243
4
bin/python
Executable file
4
bin/python
Executable file
@ -0,0 +1,4 @@
|
||||
#!/bin/bash
|
||||
|
||||
exec python3 $@
|
||||
|
3
bin/qpsh
3
bin/qpsh
@ -1,6 +1,7 @@
|
||||
#!/bin/bash
|
||||
|
||||
export QP_ROOT=$(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
22
bin/zcat
Executable file
@ -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
|
||||
|
@ -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
|
||||
|
@ -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
|
||||
|
@ -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
|
||||
|
@ -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
62
config/gfortran_macos.cfg
Normal file
@ -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
|
||||
|
@ -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
|
||||
|
@ -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
7
configure
vendored
@ -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
|
||||
|
@ -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
|
||||
|
@ -53,7 +53,6 @@ function run {
|
||||
|
||||
|
||||
@test "B-B" {
|
||||
qp set_file b2_stretched.ezfio
|
||||
run b2_stretched.zmt 1 0 6-31g
|
||||
}
|
||||
|
||||
|
@ -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
|
||||
|
||||
|
@ -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)"
|
||||
|
@ -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
|
||||
|
@ -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
|
||||
|
@ -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
|
||||
|
@ -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
|
||||
|
@ -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
|
||||
|
Loading…
Reference in New Issue
Block a user