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

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This commit is contained in:
Emmanuel Giner LCT 2023-09-26 18:26:17 +02:00
commit 6564fe2f18
10 changed files with 749 additions and 353 deletions
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62
config/flang_avx.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 : flang -ffree-line-length-none -I . -mavx -g -fPIC
LAPACK_LIB : -llapack -lblas
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED
# 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 -mavx
# 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

62
config/gfortran10.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-10 -g -ffree-line-length-none -I . -fPIC
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : DEBUG ; [ 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
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -Ofast
# Debugging flags
#################
#
# -fcheck=all : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
#
[DEBUG]
FCFLAGS : -g -msse4.2 -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurprising -Wintrinsics-std -Wno-tabs -Wintrinsic-shadow -Wline-truncation -Wreal-q-constant -Wuninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan
# OpenMP flags
#################
#
[OPENMP]
FC : -fopenmp
IRPF90_FLAGS : --openmp

62
config/gfortran_mpi_mkl.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 : mpif90 -ffree-line-length-none -I . -g -fPIC -std=legacy
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI -DSET_NESTED
# 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 -msse4.2
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -Ofast -msse4.2
# 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

63
config/ifort_2019_avx_notz.cfg Normal file
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@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --define=WITHOUT_TRAILZ --define=WITHOUT_SHIFTRL -DSET_NESTED
# 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
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback
FCFLAGS : -xAVX -O2 -ip -ftz -g
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

2
config/ifort_2019_debug.cfg
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@ -7,7 +7,7 @@
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert -DINTEL -DSET_NESTED

63
config/ifort_2021_avx_notz.cfg Normal file
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@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --define=WITHOUT_TRAILZ --define=WITHOUT_SHIFTRL
# 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
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback
FCFLAGS : -xAVX -O2 -ip -ftz -g
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

2
config/ifort_2021_debug.cfg
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@ -7,7 +7,7 @@
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert -DINTEL

696
data/basis/cc-pv5z_ecp_bfd
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68
scripts/import_champ_jastrow.py Executable file
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#!/usr/bin/env python3
conv = [ 0, 0, 2 , 6 , 13 , 23 , 37 , 55 , 78 , 106 , 140 ]
def import_jastrow(jastrow_filename):
with open(jastrow_filename,'r') as jastrow_file:
lines = [ line.strip() for line in jastrow_file.readlines() ]
lines = [ line for line in lines if line != "" ]
start = 0
end = len(lines)
for i,line in enumerate(lines):
if line.startswith("jastrow_parameter"):
start = i
elif line.startswith("end"):
end = i
lines = lines[start:end]
type_num = (len(lines)-4)//2
nord_a,nord_b,nord_c = [ int(i) for i in lines[1].split()[:3] ]
scale_k = float(lines[2].split()[0])
vec_a = []
for j in range(type_num):
vec_a += [ float(i) for i in lines[3+j].split()[:nord_a+1] ]
vec_b = [ float(i) for i in lines[3+type_num].split()[:nord_b+1] ]
vec_c = []
for j in range(type_num):
vec_c += [ float(i) for i in lines[4+type_num+j].split()[:conv[nord_c]] ]
return {
'type_num' : type_num,
'scale_k' : scale_k,
'nord_a' : nord_a,
'nord_b' : nord_b,
'nord_c' : nord_c,
'vec_a' : vec_a,
'vec_b' : vec_b,
'vec_c' : vec_c,
}
if __name__ == '__main__':
import sys
from ezfio import ezfio
ezfio.set_file(sys.argv[1])
jastrow_file = sys.argv[2]
jastrow = import_jastrow(jastrow_file)
print (jastrow)
ezfio.set_jastrow_jast_type("Qmckl")
ezfio.set_jastrow_jast_qmckl_type_nucl_num(jastrow['type_num'])
charges = ezfio.get_nuclei_nucl_charge()
types = {}
k = 0
for c in charges:
if c not in types:
types[c] = k
k += 1
type_nucl_vector = [types[c] for c in charges]
ezfio.set_jastrow_jast_qmckl_type_nucl_vector(type_nucl_vector)
ezfio.set_jastrow_jast_qmckl_rescale_ee(jastrow['scale_k'])
ezfio.set_jastrow_jast_qmckl_rescale_en([jastrow['scale_k'] for i in type_nucl_vector])
ezfio.set_jastrow_jast_qmckl_aord_num(jastrow['nord_a'])
ezfio.set_jastrow_jast_qmckl_bord_num(jastrow['nord_b'])
ezfio.set_jastrow_jast_qmckl_cord_num(jastrow['nord_c'])
ezfio.set_jastrow_jast_qmckl_c_vector_size(len(jastrow['vec_c']))
ezfio.set_jastrow_jast_qmckl_a_vector(jastrow['vec_a'])
ezfio.set_jastrow_jast_qmckl_b_vector(jastrow['vec_b'])
ezfio.set_jastrow_jast_qmckl_c_vector(jastrow['vec_c'])

22
scripts/qp_import_trexio.py
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@ -38,6 +38,15 @@ else:
QP_ROOT + "/install",
QP_ROOT + "/scripts"] + sys.path
def uint64_to_int64(u):
# Check if the most significant bit is set
if u & (1 << 63):
# Calculate the two's complement
result = -int(np.bitwise_not(np.uint64(u))+1)
else:
# The number is already positive
result = u
return result
def generate_xyz(l):
@ -133,7 +142,7 @@ def write_ezfio(trexio_filename, filename):
try:
basis_type = trexio.read_basis_type(trexio_file)
if basis_type.lower()[0] in ["g", "s"]:
if basis_type.lower() in ["gaussian", "slater"]:
shell_num = trexio.read_basis_shell_num(trexio_file)
prim_num = trexio.read_basis_prim_num(trexio_file)
ang_mom = trexio.read_basis_shell_ang_mom(trexio_file)
@ -473,8 +482,15 @@ def write_ezfio(trexio_filename, filename):
beta_s[i] = '1'
alpha_s = ''.join(alpha_s)[::-1]
beta_s = ''.join(beta_s)[::-1]
alpha = [ int(i,2) for i in qp_bitmasks.string_to_bitmask(alpha_s) ][::-1]
beta = [ int(i,2) for i in qp_bitmasks.string_to_bitmask(beta_s ) ][::-1]
def conv(i):
try:
result = np.int64(i)
except:
result = np.int64(i-2**63-1)
return result
alpha = [ uint64_to_int64(int(i,2)) for i in qp_bitmasks.string_to_bitmask(alpha_s) ][::-1]
beta = [ uint64_to_int64(int(i,2)) for i in qp_bitmasks.string_to_bitmask(beta_s ) ][::-1]
ezfio.set_determinants_bit_kind(8)
ezfio.set_determinants_n_int(1+mo_num//64)
ezfio.set_determinants_n_det(1)