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

config/flang_avx.cfg

@@ -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
+

config/gfortran10.cfg

@@ -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
+

config/gfortran_mpi_mkl.cfg

@@ -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
+

config/ifort_2019_avx_notz.cfg

@@ -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
+

config/ifort_2019_debug.cfg

@@ -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
 

config/ifort_2021_avx_notz.cfg

@@ -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
+

config/ifort_2021_debug.cfg

@@ -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
 

scripts/import_champ_jastrow.py

@@ -0,0 +1,68 @@
+#!/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'])
+

scripts/qp_import_trexio.py

@@ -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]
+    def conv(i):
-    beta  = [ int(i,2) for i in qp_bitmasks.string_to_bitmask(beta_s ) ][::-1]
+      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)