Merge pull request #65 from scemama/master

Cleaning and Davidson in MRCC

.travis.yml

@@ -7,6 +7,7 @@ python:
 before_script:
   - sudo apt-get update
   - sudo apt-get install gfortran liblapack-dev 
+  - sudo apt-get install graphviz
 
 script: 
   - ./setup_environment.sh --robot 

INSTALL.md

@@ -10,6 +10,10 @@
 * Bash
 * Patch (for opam)
 
+## Optional
+
+* graphviz
+
 
 ## Standard installation
 

data/ezfio_defaults/WILL_BE_DELETED.ezfio_default

@@ -1,61 +0,0 @@
-bielec_integrals
-  read_ao_integrals          false
-  read_mo_integrals          false
-  write_ao_integrals         false
-  write_mo_integrals         false
-  threshold_ao               1.e-15
-  threshold_mo               1.e-15
-  direct                     false
-
-cis_dressed 
-  n_state_cis                10
-  n_core_cis                 0
-  n_act_cis                  mo_basis_mo_tot_num
-  mp2_dressing               false
-  standard_doubles           true
-  en_2_2                     false
-
-determinants
-  n_states                   1
-  n_states_diag              determinants_n_states
-  n_det_max_jacobi           1000
-  threshold_generators       0.99
-  threshold_selectors        0.999
-  read_wf                    false
-  s2_eig                     false
-  only_single_double_dm      false
-
-full_ci
-  n_det_max_fci              10000
-  n_det_max_fci_property     50000
-  pt2_max                    1.e-4
-  do_pt2_end                 true
-  var_pt2_ratio              0.75
-
-cas_sd
-  n_det_max_cas_sd           100000
-  pt2_max                    1.e-4
-  do_pt2_end                 true
-  var_pt2_ratio              0.75
-
-all_singles
-  n_det_max_fci              50000
-  pt2_max                    1.e-8
-  do_pt2_end                 false
-
-hartree_fock
-  n_it_scf_max               200
-  thresh_scf                 1.e-10
-  guess                      "Huckel"
-
-cisd_selected
-  n_det_max_cisd         10000
-  pt2_max                    1.e-4
-
-cisd_sc2_selected
-  n_det_max_cisd_sc2         10000
-  pt2_max                    1.e-4
-  do_pt2_end                 true
-
-properties 
-  z_one_point                3.9

data/ezfio_defaults/cisd.ezfio_default

@@ -1,4 +0,0 @@
-cisd_selected
-  n_det_max_cisd         10000
-  pt2_max                    1.e-4
-

ocaml/qp_create_ezfio_from_xyz.ml

@@ -14,7 +14,7 @@ let spec =
   +> flag "m" (optional_with_default 1 int)
      ~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
   +> flag "p" no_arg
-     ~doc:"Using pseudo."
+     ~doc:"Using pseudopotentials"
   +> anon ("xyz_file" %: string)
 ;;
 

scripts/cache_compile.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import shelve
+import hashlib
+import re
+
+r = re.compile(ur'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)')
+p = re.compile(ur'-I IRPF90_temp/\S*\s+')
+mod = re.compile(ur'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?', re.MULTILINE | re.IGNORECASE)
+
+TMPDIR="/tmp/qp_compiler/"
+
+def main():
+    # Create temp directory
+    if "qp_compiler" not in os.listdir("/tmp"):
+      os.mkdir("/tmp/qp_compiler/")
+
+    line = sys.argv[1:]
+    command = " ".join(line)
+    command_clean = p.sub('',command)
+
+    try:
+      match = r.search(command_clean)
+      input  = match.group(1)
+      output = match.group(2)
+    except:
+      os.system(command)
+      return
+    m = hashlib.md5()
+
+    # Fread : read input
+    with open(input,'r') as file:
+      fread = file.read()
+      m.update( " ".join( [ command, fread ] ))
+
+    # Md5 Key containing command + content of Fread
+    key = TMPDIR+m.hexdigest()
+    try:
+        # Try to return the content of the .o file
+        with open(key,'r') as file:
+            result = file.read()
+    except IOError:
+        # Compile the file -> .o
+        os.system(command)
+        # Read the .o
+        with open(output,'r') as file:
+            result = file.read()
+        # Copy the .o in database
+        if not mod.search(fread.replace('\n',' ')):
+            with open(key,'w') as file:
+                file.write(result)
+        else:
+            print input+' -> module'
+    else:
+        # Write the .o file
+        with open(output,'w') as file:
+            file.write(result)
+
+if __name__ == '__main__':
+    main()

scripts/ezfio_interface/ei_handler.py

@@ -197,7 +197,7 @@ def get_dict_config_file(config_file_path, module_lower):
         * equal to MODULE_lower name by default.
     - interface  : The provider is a imput or a output
     - default : The default value /!\ stored in a Type named type!
-                   if interface == output
+                   if interface == input
     - size : Is the string read in ezfio.cgf who containt the size information
          (like 1 or =sum(ao_num))
     """
@@ -230,7 +230,8 @@ def get_dict_config_file(config_file_path, module_lower):
 
         # Create the dictionary who containt the value per default
         d_default = {"ezfio_name": pvd,
-                     "ezfio_dir": module_lower}
+                     "ezfio_dir": module_lower,
+                     "size": "1"}
 
         # Check if type if avalaible
         type_ = config_file.get(section, "type")
@@ -274,6 +275,8 @@ def get_dict_config_file(config_file_path, module_lower):
 
 
 def create_ezfio_provider(dict_ezfio_cfg):
+    import re
+
     """
     From dict d[provider_name] = {type,
                                   doc,
@@ -286,12 +289,13 @@ def create_ezfio_provider(dict_ezfio_cfg):
     output = output_dict_info['ezfio_dir'
     return [code, ...]
     """
+
     from ezfio_generate_provider import EZFIO_Provider
     dict_code_provider = dict()
 
     ez_p = EZFIO_Provider()
     for provider_name, dict_info in dict_ezfio_cfg.iteritems():
-        if "default" in dict_info:
+        if "input" in dict_info["interface"]:
             ez_p.set_type(dict_info['type'].fortran)
             ez_p.set_name(provider_name)
             ez_p.set_doc(dict_info['doc'])
@@ -299,6 +303,9 @@ def create_ezfio_provider(dict_ezfio_cfg):
             ez_p.set_ezfio_name(dict_info['ezfio_name'])
             ez_p.set_output("output_%s" % dict_info['ezfio_dir'])
 
+            # (nuclei.nucl_num,pseudo.klocmax) => (nucl_num,klocmax)
+            ez_p.set_size(re.sub(r'\w+\.', "", dict_info['size']))
+
             dict_code_provider[provider_name] = str(ez_p) + "\n"
 
     return dict_code_provider
@@ -342,15 +349,32 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
     def size_format_to_ezfio(size_raw):
         """
         If size_raw == "=" is a formula -> do nothing; return
+        Else convert the born of a multidimential array
+           (12,begin:end) into (12,begin+end+1) for example
         If the value are between parenthses ->  do nothing; return
-        Else put it in parenthsesis
         """
 
         size_raw = str(size_raw)
-        if any([size_raw.startswith('='),
+        if size_raw.startswith('='):
-                size_raw.startswith("(") and size_raw.endswith(")")]):
             size_convert = size_raw
         else:
+            size_raw = provider_info["size"].translate(None, "()")
+            size_raw = size_raw.replace('.', '_')
+
+            a_size_raw = []
+            for dim in size_raw.split(","):
+                try:
+                    (begin, end) = map(str.strip, dim.split(":"))
+                except ValueError:
+                    a_size_raw.append(dim)
+                else:
+                    if begin[0] == '-':
+                        a_size_raw.append("{0}+{1}+1".format(end, begin[1:]))
+                    else:
+                       a_size_raw.append("{0}-{1}+1".format(end, begin))
+
+            size_raw = ",".join(a_size_raw)
+
             size_convert = "({0})".format(size_raw)
         return size_convert
 
@@ -719,7 +743,6 @@ def save_ocaml_qp_edit(str_ocaml_qp_edit):
 
 if __name__ == "__main__":
     arguments = docopt(__doc__)
-
     # ___
     #  |  ._  o _|_
     # _|_ | | |  |_

scripts/ezfio_interface/ezfio_generate_provider.py

@@ -10,10 +10,11 @@ fetched from the EZFIO file.
 
 import sys
 
+
 class EZFIO_Provider(object):
 
     data = """
-BEGIN_PROVIDER [ %(type)s, %(name)s ]
+BEGIN_PROVIDER [ %(type)s, %(name)s %(size)s ]
   implicit none
   BEGIN_DOC
 ! %(doc)s
@@ -48,6 +49,9 @@ END_PROVIDER
                 msg = "Error : %s is not set in EZFIO.cfg" % (v)
                 print >>sys.stderr, msg
                 sys.exit(1)
+        if "size" not in self.__dict__:
+            self.__dict__["size"] = ""
+
         return self.data % self.__dict__
 
     def set_write(self):
@@ -83,6 +87,12 @@ END_PROVIDER
     def set_output(self, t):
         self.output = t
 
+    def set_size(self, t):
+
+        if t != "1":
+            self.size = ", " + t
+        else:
+            self.size = ""
 
 def test_module():
     T = EZFIO_Provider()

scripts/ezfio_interface/qp_convert_ezfio_v1_to_v2.sh

@@ -15,10 +15,10 @@ mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null
 # Set disk_acess
 echo "Change {read,write}_ao_integrals > disk_access_ao_integrals"
 
-biint=$1/bielec_integrals
+biint=$1/Integrals_bielec
 
 if [[ -f  $biint/read_ao_integrals ]]; then
-    if [[ `cat $1/bielec_integrals/read_ao_integrals` -eq "T" ]]
+    if [[ `cat $1/Integrals_bielec/read_ao_integrals` -eq "T" ]]
     then
             echo "Read" > $biint/disk_access_ao_integrals
     
@@ -33,4 +33,6 @@ if [[ -f  $biint/read_ao_integrals ]]; then
     rm $biint/read_ao_integrals  $biint/write_ao_integrals  $biint/write_ao_intergals 2> /dev/null
 fi
 
+mv $1/MonoInts $1/Integrals_Monoelec
+
 echo "Done"

scripts/ezfio_interface/qp_convert_output_to_ezfio.py

@@ -273,7 +273,7 @@ def write_ezfio(res, filename):
     # \_|  |___/\___|\__,_|\__,_|\___/
     #
 
-    ezfio.set_pseudo_integrals_do_pseudo(False)
+    ezfio.set_pseudo_do_pseudo(False)
 
 
 def get_full_path(file_path):

scripts/install/install_m4.sh

@@ -16,6 +16,7 @@ fi
 
 cd ${QPACKAGE_ROOT}
 
+rm -f l${QPACKAGE_ROOT}/bin/m4
 if [[ -z ${M4} ]] 
 then 
     rm -f -- bin/m4

scripts/module/module_handler.py

@@ -121,7 +121,12 @@ def create_png_from_path(path):
     "path = /home/razoa/quantum_package/src/Molden/NEEDED_CHILDREN_MODULES"
 
     l_module = os.path.split(path)[0].split("/")[-1]
-    create_png([l_module])
+
+    import pydot
+    try:
+        create_png([l_module])
+    except pydot.InvocationException:
+        pass
 
 
 def create_png(l_module):
@@ -154,8 +159,10 @@ def create_png(l_module):
         draw_module_edge(module, d_ref[module])
 
     # Save
-    path = '{0}.png'.format("_".join(l_module))
+    path = '{0}.png'.format("tree_dependancy")
-    print "png saved in {0}".format(path)
+    # path = '{0}.png'.format("_".join(l_module))
+    # print "png saved in {0}".format(path)
+
     graph.write_png(path)
 
 if __name__ == '__main__':

scripts/module/pydot.py

@@ -31,7 +31,8 @@ import sys
 try:
     import dot_parser
 except Exception as e:
-    print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible."
+    pass
+    # print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible."
 
 
 GRAPH_ATTRIBUTES = set(['Damping', 'K', 'URL', 'aspect', 'bb', 'bgcolor',

scripts/pseudo/put_pseudo_in_ezfio.py

@@ -186,7 +186,7 @@ def add_zero(array, size, type):
 
 def make_it_square(matrix, dim, type=float):
     """
-    matix the matrix to squate
+    matix the matrix to square
     dim array  [lmax, kmax]
     type the null value you want
         [[[28.59107316], [19.37583724]], [[50.25646328]]]
@@ -311,11 +311,11 @@ if __name__ == "__main__":
     # ~#~#~#~#~ #
 
     klocmax = max([len(i) for i in v_k])
-    ezfio.pseudo_integrals_klocmax = klocmax
+    ezfio.pseudo_pseudo_klocmax = klocmax
 
-    ezfio.pseudo_integrals_v_k = zip(*v_k)
+    ezfio.pseudo_pseudo_v_k = zip(*v_k)
-    ezfio.pseudo_integrals_n_k = zip(*n_k)
+    ezfio.pseudo_pseudo_n_k = zip(*n_k)
-    ezfio.pseudo_integrals_dz_k = zip(*dz_k)
+    ezfio.pseudo_pseudo_dz_k = zip(*dz_k)
 
     # ~#~#~#~#~#~#~#~#~ #
     # N o n _ L o c a l #
@@ -324,15 +324,15 @@ if __name__ == "__main__":
     lmax = max([len(i) for i in v_kl])
     kmax = max([len(sublist) for list_ in v_kl for sublist in list_])
 
-    ezfio.pseudo_integrals_lmaxpo = lmax
+    ezfio.pseudo_pseudo_lmax = lmax - 1
-    ezfio.pseudo_integrals_kmax = kmax
+    ezfio.pseudo_pseudo_kmax = kmax
 
     v_kl = make_it_square(v_kl, [lmax, kmax])
     n_kl = make_it_square(n_kl, [lmax, kmax], int)
     dz_kl = make_it_square(dz_kl, [lmax, kmax])
 
-    ezfio.pseudo_integrals_v_kl = zip(*v_kl)
+    ezfio.pseudo_pseudo_v_kl = zip(*v_kl)
-    ezfio.pseudo_integrals_n_kl = zip(*n_kl)
+    ezfio.pseudo_pseudo_n_kl = zip(*n_kl)
-    ezfio.pseudo_integrals_dz_kl = zip(*dz_kl)
+    ezfio.pseudo_pseudo_dz_kl = zip(*dz_kl)
 
-    ezfio.pseudo_integrals_do_pseudo = True
+    ezfio.pseudo_do_pseudo = True

scripts/run_Makefile_common.sh

@@ -66,3 +66,6 @@ ${QPACKAGE_ROOT}/scripts/module/create_Makefile_depend.sh
 
 # Update EZFIO interface
 ${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py
+
+# Create png
+${QPACKAGE_ROOT}/scripts/module/module_handler.py create_png

scripts/update_README.py

@@ -2,7 +2,7 @@
 
 """Updates the README.rst file as the include directive is disabled on GitHub."""
 __date__ = "Thu Apr  3 23:06:18 CEST 2014"
-__author__ = "Anthony Scemama <scemama@irsamc.ups-tlse.fr>"
+__author__ = "Anthony Scemama<scemama@irsamc.ups-tlse.fr>  & TApplencourt "
 
 
 README = "README.rst"
@@ -21,12 +21,6 @@ header = """
 
 """
 
-try:
-    # subprocess.check_output("git status".split())
-    has_git = True
-except OSError:
-    has_git = False
-
 
 def fetch_splitted_data():
     """Read the README.rst file and split it in strings:
@@ -87,10 +81,12 @@ def update_needed(data):
     modules = file.read()
     file.close()
 
+    header_image = ".. image:: tree_dependancy.png\n\n"
+
     if modules.strip() != "":
         modules = ['* `%s <%s%s>`_' % (x, URL, x) for x in modules.split()]
         modules = "\n".join(modules)
-        modules = Needed_key + header + modules + '\n\n'
+        modules = Needed_key + header + header_image + modules + '\n\n'
 
     has_modules = False
     for i in range(len(data)):

setup_environment.sh

@@ -28,7 +28,7 @@ EOF
 
 
 source quantum_package.rc
-
+mkdir -p install_logs
 echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}"
 ${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh     | tee ${QPACKAGE_ROOT}/install_logs/install_irpf90.log
 if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]]  ||  [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]] ||  [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]]

src/AOs/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-Nuclei
+Nuclei Utils

src/AOs/README.rst

@@ -39,7 +39,10 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============
@@ -144,5 +147,11 @@ Documentation
   Per convention, for P,D,F and G AOs, we take the index
   of the AO with the the corresponding power in the "X" axis
 
+`n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L2>`_
+  Undocumented
+
+`n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L1>`_
+  Undocumented
+
 
 

src/Bielec_integrals/NEEDED_CHILDREN_MODULES

@@ -1 +0,0 @@
-MonoInts Bitmask

src/Bitmask/README.rst

@@ -40,6 +40,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 
 Documentation

src/Bitmask/bitmasks_module.f90

@@ -8,4 +8,4 @@ module bitmasks
   integer, parameter             :: d_part2 = 4
   integer, parameter             :: s_hole  = 5
   integer, parameter             :: s_part  = 6
-end module
+end module bitmasks

src/CAS_SD/EZFIO.cfg

@@ -1,29 +1,3 @@
-[N_det_max_cas_sd]
-type: Det_number_max
-doc: Max number of determinants in the wave function
-interface: input
-default: 10000
-
-[do_pt2_end]
-type: logical
-doc: If true, compute the PT2 at the end of the selection
-interface: input
-default: True
-
-[PT2_max]
-type: PT2_energy
-doc: The selection process stops when the largest PT2 (for all the state is lower
-     than pt2_max in absolute value
-interface: input
-default: 0.0001
-
-[var_pt2_ratio]
-type: Normalized_float
-doc: The selection process stops when the energy ratio variational/(variational+PT2)
-     is equal to var_pt2_ratio
-interface: input
-default: 0.75
-
 [energy]
 type: double precision
 doc: "Calculated CAS-SD energy"

src/CAS_SD/README.rst

@@ -24,6 +24,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_

src/CAS_SD/cas_sd.irp.f

@@ -13,12 +13,12 @@ program full_ci
   N_det_old = 0
   pt2 = 1.d0
   diag_algorithm = "Lapack"
-  if (N_det > n_det_max_cas_sd) then
+  if (N_det > N_det_max) then
     call diagonalize_CI
     call save_wavefunction
     psi_det = psi_det_sorted
     psi_coef = psi_coef_sorted
-    N_det = n_det_max_cas_sd
+    N_det = N_det_max
     soft_touch N_det psi_det psi_coef
     call diagonalize_CI
     call save_wavefunction
@@ -30,7 +30,7 @@ program full_ci
     print *,  '-----'
   endif
 
-  do while (N_det < n_det_max_cas_sd.and.maxval(abs(pt2(1:N_st))) > pt2_max)
+  do while (N_det < N_det_max.and.maxval(abs(pt2(1:N_st))) > pt2_max)
     N_det_old = N_det
     call H_apply_CAS_SD(pt2, norm_pert, H_pert_diag,  N_st)
 
@@ -38,10 +38,10 @@ program full_ci
     PROVIDE  psi_det
     PROVIDE  psi_det_sorted
 
-    if (N_det > n_det_max_cas_sd) then
+    if (N_det > N_det_max) then
        psi_det = psi_det_sorted
        psi_coef = psi_coef_sorted
-       N_det = n_det_max_cas_sd
+       N_det = N_det_max
        soft_touch N_det psi_det psi_coef
     endif
     call diagonalize_CI

src/CAS_SD/cas_sd_selected.irp.f

@@ -12,12 +12,12 @@ program full_ci
   
   pt2 = 1.d0
   diag_algorithm = "Lapack"
-  if (N_det > n_det_max_cas_sd) then
+  if (N_det > N_det_max) then
     call diagonalize_CI
     call save_wavefunction
     psi_det = psi_det_sorted
     psi_coef = psi_coef_sorted
-    N_det = n_det_max_cas_sd
+    N_det = N_det_max
     soft_touch N_det psi_det psi_coef
     call diagonalize_CI
     call save_wavefunction
@@ -29,17 +29,17 @@ program full_ci
     print *,  '-----'
   endif
 
-  do while (N_det < n_det_max_cas_sd.and.maxval(abs(pt2(1:N_st))) > pt2_max)
+  do while (N_det < N_det_max.and.maxval(abs(pt2(1:N_st))) > pt2_max)
     call H_apply_CAS_SD_selected(pt2, norm_pert, H_pert_diag,  N_st)
 
     PROVIDE  psi_coef
     PROVIDE  psi_det
     PROVIDE  psi_det_sorted
 
-    if (N_det > n_det_max_cas_sd) then
+    if (N_det > N_det_max) then
        psi_det = psi_det_sorted
        psi_coef = psi_coef_sorted
-       N_det = n_det_max_cas_sd
+       N_det = N_det_max
        soft_touch N_det psi_det psi_coef
     endif
     call diagonalize_CI

src/CID/README.rst

@@ -15,6 +15,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 

src/CID_SC2_selected/README.rst

@@ -19,5 +19,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `CID_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected>`_
 

src/CID_selected/README.rst

@@ -22,6 +22,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `CID <http://github.com/LCPQ/quantum_package/tree/master/src/CID>`_
 

src/CIS/README.rst

@@ -31,6 +31,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 

src/CISD/README.rst

@@ -15,6 +15,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 

src/CISD_SC2_selected/EZFIO.cfg

@@ -1,22 +1,3 @@
-[N_det_max_cisd_sc2]
-type: Det_number_max
-doc: Max number of determinants
-interface: input
-default: 10000
-
-[do_pt2_end]
-type: logical
-doc: If true, compute the PT2 at the end of the selection
-interface: input
-default: True
-
-[PT2_max]
-type: PT2_energy
-doc: The selection process stops when the largest PT2 (for all the states) is lower
-     than abs(pt2_max)
-interface: input
-default: 0.0001
-
 [energy]
 type: double precision
 doc: Calculated CISD_SC2 energy of ground_state

src/CISD_SC2_selected/README.rst

@@ -19,5 +19,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
 

src/CISD_SC2_selected/cisd_sc2_selection.irp.f

@@ -15,12 +15,12 @@ program cisd_sc2_selected
                  
   E_old(1) = HF_energy
   davidson_threshold = 1.d-10
-  if (N_det > n_det_max_cisd_sc2) then
+  if (N_det > N_det_max) then
     call diagonalize_CI_SC2
     call save_wavefunction
     psi_det = psi_det_sorted
     psi_coef = psi_coef_sorted
-    N_det = n_det_max_cisd_sc2
+    N_det = N_det_max
     soft_touch N_det psi_det psi_coef
     call diagonalize_CI
     call save_wavefunction
@@ -34,7 +34,7 @@ program cisd_sc2_selected
 
   integer :: i_count
   i_count = 0
-  do while (N_det < n_det_max_cisd_sc2.and.maxval(abs(pt2(1:N_st))) > pt2_max)
+  do while (N_det < N_det_max.and.maxval(abs(pt2(1:N_st))) > pt2_max)
     print*,'----'
     print*,''
     call H_apply_SC2_selected(pt2, norm_pert, H_pert_diag,  N_st)
@@ -70,7 +70,7 @@ program cisd_sc2_selected
     call ezfio_set_full_ci_energy(CI_SC2_energy(1))
 
   enddo
-  N_det = min(n_det_max_cisd_sc2,N_det)
+  N_det = min(N_det_max,N_det)
   davidson_threshold = 1.d-10
   touch N_det psi_det psi_coef davidson_threshold davidson_criterion
   call diagonalize_CI_SC2

src/CISD_selected/README.rst

@@ -14,12 +14,6 @@ Documentation
 `cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/cisd_selection.irp.f#L1>`_
   Undocumented
 
-`n_det_max_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/options.irp.f#L1>`_
-  Get n_det_max_cisd from EZFIO file
-
-`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/options.irp.f#L18>`_
-  Get pt2_max from EZFIO file
-
 
 
 Needed Modules
@@ -28,6 +22,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
 

src/CISD_selected/cisd.ezfio_config

@@ -1,3 +0,0 @@
-cisd_selected
-  n_det_max_cisd  integer 
-  pt2_max             double precision

src/CISD_selected/cisd_selection.irp.f

@@ -18,7 +18,7 @@ program cisd
    print *,  'E                            = ', CI_energy(i) 
   enddo
   E_old = CI_energy
-  do while (maxval(abs(pt2(1:N_st))) > pt2_max.and.n_det < n_det_max_cisd)
+  do while (maxval(abs(pt2(1:N_st))) > pt2_max.and.n_det < N_det_max)
     print*,'----'
     print*,''
     call H_apply_cisd_selection(perturbation,pt2, norm_pert, H_pert_diag,  N_st)
@@ -38,7 +38,7 @@ program cisd
       exit
     endif
   enddo
-  N_det = min(N_det,n_det_max_cisd)
+  N_det = min(N_det,N_det_max)
   touch N_det psi_det psi_coef
   call diagonalize_CI
   deallocate(pt2,norm_pert,H_pert_diag)

src/CISD_selected/options.irp.f

@@ -1,34 +0,0 @@
-  BEGIN_PROVIDER [ integer, n_det_max_cisd ]
-   implicit none
-   BEGIN_DOC
-  ! Get n_det_max_cisd from EZFIO file
-   END_DOC
-   logical :: has_n_det_max_cisd
-   PROVIDE ezfio_filename
-   call ezfio_has_cisd_selected_n_det_max_cisd(has_n_det_max_cisd)
-   if (has_n_det_max_cisd) then
-     call ezfio_get_cisd_selected_n_det_max_cisd(n_det_max_cisd)
-   else
-     n_det_max_cisd = 30000
-     call ezfio_set_cisd_selected_n_det_max_cisd(n_det_max_cisd)
-   endif
-   print*,'n_det_max_cisd = ',n_det_max_cisd
-  END_PROVIDER
-
-  BEGIN_PROVIDER [ double precision , pt2_max ]
-   implicit none
-   BEGIN_DOC
-  ! Get pt2_max from EZFIO file
-   END_DOC
-   logical :: has_pt2_max
-   PROVIDE ezfio_filename
-   call ezfio_has_cisd_selected_pt2_max(has_pt2_max)
-   if (has_pt2_max) then
-     call ezfio_get_cisd_selected_pt2_max(pt2_max)
-   else
-     pt2_max = 1.d-9
-     call ezfio_set_cisd_selected_pt2_max(pt2_max)
-   endif
-   print*,'pt2_max = ',pt2_max
-  END_PROVIDER
-

src/DDCI_selected/README.rst

@@ -19,6 +19,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_

src/DDCI_selected/ddci.irp.f

@@ -11,12 +11,12 @@ program full_ci
   
   pt2 = 1.d0
   diag_algorithm = "Lapack"
-  if (N_det > n_det_max_fci) then
+  if (N_det > N_det_max) then
     call diagonalize_CI
     call save_wavefunction
     psi_det = psi_det_sorted
     psi_coef = psi_coef_sorted
-    N_det = n_det_max_fci
+    N_det = N_det_max
     soft_touch N_det psi_det psi_coef
     call diagonalize_CI
     call save_wavefunction
@@ -28,17 +28,17 @@ program full_ci
     print *,  '-----'
   endif
 
-  do while (N_det < n_det_max_fci.and.maxval(abs(pt2(1:N_st))) > pt2_max)
+  do while (N_det < N_det_max.and.maxval(abs(pt2(1:N_st))) > pt2_max)
     call H_apply_DDCI_selection(pt2, norm_pert, H_pert_diag,  N_st)
 
     PROVIDE  psi_coef
     PROVIDE  psi_det
     PROVIDE  psi_det_sorted
 
-    if (N_det > n_det_max_fci) then
+    if (N_det > N_det_max) then
        psi_det = psi_det_sorted
        psi_coef = psi_coef_sorted
-       N_det = n_det_max_fci
+       N_det = N_det_max
        soft_touch N_det psi_det psi_coef
     endif
     call diagonalize_CI

src/DDCI_selected/options.irp.f

@@ -1,32 +0,0 @@
-BEGIN_SHELL [ /usr/bin/python ]
-from ezfio_with_default import EZFIO_Provider
-T = EZFIO_Provider()
-T.set_type      ( "integer" )
-T.set_name      ( "N_det_max_fci" )
-T.set_doc       ( "Max number of determinants in the wave function" )
-T.set_ezfio_dir ( "full_ci" )
-T.set_ezfio_name( "N_det_max_fci" )
-T.set_output    ( "output_full_ci" )
-print T
-
-T.set_type      ( "logical" )
-T.set_name      ( "do_pt2_end" )
-T.set_doc       ( "If true, compute the PT2 at the end of the selection" )
-T.set_ezfio_name( "do_pt2_end" )
-print T
-
-T.set_type      ( "double precision" )
-T.set_name      ( "pt2_max" )
-T.set_doc       ( """The selection process stops when the largest PT2 (for all the states) 
-is lower than pt2_max in absolute value""" )
-T.set_ezfio_name( "pt2_max" )
-print T
-
-T.set_type      ( "double precision" )
-T.set_name      ( "var_pt2_ratio" )
-T.set_doc       ( """The selection process stops when the energy ratio variational/(variational+PT2)
-is equal to var_pt2_ratio""" )
-T.set_ezfio_name( "var_pt2_ratio" )
-print T
-END_SHELL
-

src/DensityFit/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+AOs Pseudo

src/DensityFit/README.rst

@@ -0,0 +1,70 @@
+=================
+DensityFit Module
+=================
+
+In this module, the basis of all the products of atomic orbitals is built.
+
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`aux_basis_coef <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L94>`_
+  Exponents and coefficients of the auxiliary basis
+
+`aux_basis_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L37>`_
+  Exponents of the auxiliary basis
+
+`aux_basis_expo <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L93>`_
+  Exponents and coefficients of the auxiliary basis
+
+`aux_basis_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L36>`_
+  Exponents of the auxiliary basis
+
+`aux_basis_idx <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L20>`_
+  aux_basis_idx(k) -> i,j
+
+`aux_basis_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L40>`_
+  Exponents of the auxiliary basis
+
+`aux_basis_num <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L2>`_
+  Number of auxiliary basis functions
+
+`aux_basis_num_8 <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L3>`_
+  Number of auxiliary basis functions
+
+`aux_basis_num_sqrt <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L1>`_
+  Number of auxiliary basis functions
+
+`aux_basis_overlap_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L69>`_
+  Auxiliary basis set
+
+`aux_basis_power <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L39>`_
+  Exponents of the auxiliary basis
+
+`aux_basis_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L38>`_
+  Exponents of the auxiliary basis
+
+`aux_basis_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L111>`_
+  = ao_prim_num_max
+
+`save_aux_basis <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/aux_basis.irp.f#L120>`_
+  Undocumented
+
+`aux_basis_four_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit/overlap.irp.f#L1>`_
+  \int \chi_i(r) \chi_j(r) \chi_k(r) \chi_l(r) dr
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+.. image:: tree_dependancy.png
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
+

src/DensityFit/aux_basis.ezfio_config

@@ -0,0 +1,12 @@
+aux_basis
+  aux_basis_num             integer
+  aux_basis_num_sqrt        integer
+  aux_basis_idx             integer       (2,aux_basis_aux_basis_num)
+  aux_basis_prim_num        integer       (aux_basis_aux_basis_num_sqrt)
+  aux_basis_nucl            integer       (aux_basis_aux_basis_num_sqrt)
+  aux_basis_power           integer       (aux_basis_aux_basis_num_sqrt,3)
+  aux_basis_prim_num_max    integer       = maxval(aux_basis_aux_basis_prim_num)
+  aux_basis_coef            double precision (aux_basis_aux_basis_num_sqrt,aux_basis_aux_basis_prim_num_max)
+  aux_basis_expo            double precision (aux_basis_aux_basis_num_sqrt,aux_basis_aux_basis_prim_num_max)
+
+

src/DensityFit/aux_basis.irp.f

@@ -0,0 +1,130 @@
+ BEGIN_PROVIDER [ integer, aux_basis_num_sqrt ]
+&BEGIN_PROVIDER [ integer, aux_basis_num ]
+&BEGIN_PROVIDER [ integer, aux_basis_num_8 ]
+ implicit none
+ BEGIN_DOC
+ ! Number of auxiliary basis functions
+ END_DOC
+ integer :: align_double
+
+ if (do_pseudo) then
+!   aux_basis_num_sqrt = ao_num + ao_pseudo_num
+   aux_basis_num_sqrt = ao_num 
+ else
+ endif
+
+ aux_basis_num = aux_basis_num_sqrt * (aux_basis_num_sqrt+1)/2 
+ aux_basis_num_8 = align_double(aux_basis_num)
+END_PROVIDER
+
+BEGIN_PROVIDER [ integer, aux_basis_idx, (2,aux_basis_num) ]
+ implicit none
+ BEGIN_DOC
+! aux_basis_idx(k) -> i,j
+ END_DOC
+ integer :: i,j,k
+ k=0
+ do j=1,aux_basis_num_sqrt
+   do i=1,j
+     k = k+1
+     aux_basis_idx(1,k) = i
+     aux_basis_idx(2,k) = j
+   enddo
+ enddo
+END_PROVIDER
+
+ BEGIN_PROVIDER [ double precision, aux_basis_expo_transp, (ao_prim_num_max_align,aux_basis_num_sqrt) ]
+&BEGIN_PROVIDER [ double precision, aux_basis_coef_transp, (ao_prim_num_max_align,aux_basis_num_sqrt) ]
+&BEGIN_PROVIDER [ integer, aux_basis_prim_num, (aux_basis_num_sqrt) ]
+&BEGIN_PROVIDER [ integer, aux_basis_power, (aux_basis_num_sqrt,3) ]
+&BEGIN_PROVIDER [ integer, aux_basis_nucl, (aux_basis_num_sqrt) ]
+ implicit none
+ BEGIN_DOC
+ ! Exponents of the auxiliary basis
+ END_DOC
+ integer                        :: i,j
+ do j=1,ao_num
+   do i=1,ao_prim_num_max
+     aux_basis_expo_transp(i,j) = ao_expo_ordered_transp(i,j)
+     aux_basis_coef_transp(i,j) = ao_coef_normalized_ordered_transp(i,j)
+   enddo
+ enddo
+ do i=1,ao_num
+   aux_basis_prim_num(i) = ao_prim_num(i)
+   aux_basis_nucl(i) = ao_nucl(i)
+   aux_basis_power(i,1:3) = ao_power(i,1:3)
+ enddo
+
+! do j=1,ao_pseudo_num
+!   aux_basis_expo_transp(1,ao_num+j) = 0.5d0*pseudo_ao_expo(j)
+!   aux_basis_coef_transp(1,ao_num+j) = 1.d0
+!   aux_basis_power(ao_num+j,1:3) = 0
+!   aux_basis_prim_num(ao_num+j) = 1
+!   aux_basis_nucl(ao_num+j) = pseudo_ao_nucl(j)
+! enddo
+  
+END_PROVIDER
+
+
+BEGIN_PROVIDER [ double precision, aux_basis_overlap_matrix, (aux_basis_num_8,aux_basis_num) ]
+ implicit none
+ BEGIN_DOC  
+! Auxiliary basis set
+ END_DOC
+ integer :: m,n,i,j,k,l
+ double precision :: aux_basis_four_overlap
+
+ aux_basis_overlap_matrix(1,1) = aux_basis_four_overlap(1,1,1,1)
+ !$OMP PARALLEL DO PRIVATE(i,j,k,l,m,n) SCHEDULE(GUIDED)
+ do m=1,aux_basis_num
+   i = aux_basis_idx(1,m)
+   j = aux_basis_idx(2,m)
+   do n=1,m
+     k = aux_basis_idx(1,n)
+     l = aux_basis_idx(2,n)
+     aux_basis_overlap_matrix(m,n) = aux_basis_four_overlap(i,j,k,l)
+     aux_basis_overlap_matrix(n,m) = aux_basis_overlap_matrix(m,n) 
+   enddo
+ enddo
+ !$OMP END PARALLEL DO
+
+END_PROVIDER
+
+ BEGIN_PROVIDER [ double precision, aux_basis_expo, (aux_basis_num_sqrt,aux_basis_prim_num_max) ]
+&BEGIN_PROVIDER [ double precision, aux_basis_coef, (aux_basis_num_sqrt,aux_basis_prim_num_max) ]
+ implicit none
+ BEGIN_DOC
+ ! Exponents and coefficients of the auxiliary basis
+ END_DOC
+ integer :: i,j
+ aux_basis_expo = 0.d0
+ aux_basis_coef = 0.d0
+ do j=1,aux_basis_num_sqrt
+   do i=1,aux_basis_prim_num(j)
+     aux_basis_expo(j,i) = aux_basis_expo_transp(i,j)
+     aux_basis_coef(j,i) = aux_basis_coef_transp(i,j)
+   enddo
+ enddo
+
+END_PROVIDER
+
+BEGIN_PROVIDER [ integer, aux_basis_prim_num_max ]
+ implicit none
+ BEGIN_DOC
+ ! = ao_prim_num_max
+ END_DOC
+ aux_basis_prim_num_max = ao_prim_num_max
+END_PROVIDER
+
+
+subroutine save_aux_basis
+ implicit none
+ call ezfio_set_aux_basis_aux_basis_num(aux_basis_num)
+ call ezfio_set_aux_basis_aux_basis_num_sqrt(aux_basis_num_sqrt)
+ call ezfio_set_aux_basis_aux_basis_idx(aux_basis_idx)
+ call ezfio_set_aux_basis_aux_basis_prim_num(aux_basis_prim_num)
+ call ezfio_set_aux_basis_aux_basis_nucl(aux_basis_nucl)
+ call ezfio_set_aux_basis_aux_basis_power(aux_basis_power)
+ call ezfio_set_aux_basis_aux_basis_coef(aux_basis_coef)
+ call ezfio_set_aux_basis_aux_basis_expo(aux_basis_expo)
+end

src/DensityFit/overlap.irp.f

@@ -0,0 +1,66 @@
+double precision function aux_basis_four_overlap(i,j,k,l)
+  implicit none
+  BEGIN_DOC
+! \int \chi_i(r) \chi_j(r) \chi_k(r) \chi_l(r) dr
+  END_DOC
+  integer,intent(in)             :: i,j,k,l
+  integer                        :: p,q,r,s
+  double precision               :: I_center(3),J_center(3),K_center(3),L_center(3)
+  integer                        :: num_i,num_j,num_k,num_l,dim1,I_power(3),J_power(3),K_power(3),L_power(3)
+  double precision               :: overlap_x,overlap_y,overlap_z, overlap
+  include 'include/constants.F'
+  double precision               :: P_new(0:max_dim,3),P_center(3),fact_p,pp
+  double precision               :: Q_new(0:max_dim,3),Q_center(3),fact_q,qq
+  integer                        :: iorder_p(3), iorder_q(3)
+  
+  dim1 = n_pt_max_integrals
+  
+  num_i = aux_basis_nucl(i)
+  num_j = aux_basis_nucl(j)
+  num_k = aux_basis_nucl(k)
+  num_l = aux_basis_nucl(l)
+  aux_basis_four_overlap = 0.d0
+  
+  do p = 1, 3
+    I_power(p) = aux_basis_power(i,p)
+    J_power(p) = aux_basis_power(j,p)
+    K_power(p) = aux_basis_power(k,p)
+    L_power(p) = aux_basis_power(l,p)
+    I_center(p) = nucl_coord(num_i,p)
+    J_center(p) = nucl_coord(num_j,p)
+    K_center(p) = nucl_coord(num_k,p)
+    L_center(p) = nucl_coord(num_l,p)
+  enddo
+  
+  do p = 1, aux_basis_prim_num(i)
+    double precision               :: coef1
+    coef1 = aux_basis_coef_transp(p,i)
+    do q = 1, aux_basis_prim_num(j)
+      call give_explicit_poly_and_gaussian(P_new,P_center,pp,fact_p,iorder_p,&
+          aux_basis_expo_transp(p,i),aux_basis_expo_transp(q,j),                 &
+          I_power,J_power,I_center,J_center,dim1)
+      double precision               :: coef2
+      coef2 = coef1*aux_basis_coef_transp(q,j)*fact_p
+      do r = 1, aux_basis_prim_num(k)
+        double precision               :: coef3
+        coef3 = coef2*aux_basis_coef_transp(r,k)
+        do s = 1, aux_basis_prim_num(l)
+          double precision               :: general_primitive_integral
+          call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,    &
+              aux_basis_expo_transp(r,k),aux_basis_expo_transp(s,l),             &
+              K_power,L_power,K_center,L_center,dim1)
+          double precision               :: coef4
+          coef4 = coef3*aux_basis_coef_transp(s,l)*fact_q
+          call overlap_gaussian_xyz(P_center,Q_center,pp,qq,iorder_p,iorder_q,overlap_x,overlap_y,overlap_z,overlap,dim1)
+          aux_basis_four_overlap +=  coef4 * overlap 
+        enddo ! s
+      enddo  ! r
+    enddo   ! q
+  enddo    ! p
+    
+end
+
+! TODO : Schwartz acceleration
+
+
+

src/Determinants/EZFIO.cfg

@@ -1,15 +1,27 @@
+[N_det_max]
+type: Det_number_max
+doc: Max number of determinants in the wave function
+interface: input
+default: 10000
+
+[N_det_max_property]
+type: Det_number_max
+doc: Max number of determinants in the wave function when you select for a given property
+interface: input
+default: 10000
+
+[N_det_max_jacobi]
+type: Det_number_max
+doc: Maximum number of determinants diagonalized by Jacobi
+interface: input
+default: 1000
+
 [N_states]
 type: States_number
 doc: Number of states to consider
 interface: input
 default: 1
 
-[N_det_max_jacobi]
-type: Strictly_positive_int
-doc: Maximum number of determinants diagonalized by Jacobi
-interface: input
-default: 1000
-
 [read_wf]
 type: logical
 doc: If true, read the wave function from the EZFIO file
@@ -40,9 +52,6 @@ doc: Thresholds on selectors (fraction of the norm)
 interface: input
 default:        0.999
 
-
-# Only create the ezfio_config, (no Input_* and no PROVIDER)
-
 [n_states_diag]
 type: integer
 doc: n_states_diag
@@ -72,13 +81,13 @@ type: integer
 interface: OCaml
 doc: psi_coef
 type: double precision 
-size: (determinants_n_det,determinants_n_states)
+size: (determinants.n_det,determinants.n_states)
 
 [psi_det]
 interface: OCaml
 doc: psi_det
 type: integer*8
-size: (determinants_n_int*determinants_bit_kind/8,2,determinants_n_det)
+size: (determinants.n_int*determinants.bit_kind/8,2,determinants.n_det)
 
 [det_num]
 interface: OCaml
@@ -89,13 +98,13 @@ type: integer
 interface: OCaml
 doc: det_occ
 type: integer          
-size:  (electrons_elec_alpha_num,determinants_det_num,2)
+size:  (electrons.elec_alpha_num,determinants.det_num,2)
 
 [det_coef]
 interface: OCaml
 doc: det_coef
 type: double precision 
-size:  (determinants_det_num)
+size:  (determinants.det_num)
 
 [expected_s2]
 interface: OCaml

src/Determinants/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-Bielec_integrals
+Integrals_Monoelec Integrals_Bielec 

src/Determinants/README.rst

@@ -32,7 +32,10 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+.. image:: tree_dependancy.png
+
+* `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
+* `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
 
 Documentation
 =============
@@ -529,12 +532,6 @@ Documentation
 `save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_casino.irp.f#L1>`_
   Undocumented
 
-`save_dets_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_qmcchem.irp.f#L1>`_
-  Undocumented
-
-`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_qmcchem.irp.f#L46>`_
-  Undocumented
-
 `save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_natorb.irp.f#L1>`_
   Undocumented
 

src/Determinants/save_for_qmcchem.irp.f

@@ -1,51 +0,0 @@
-subroutine save_dets_qmcchem
- use bitmasks
- implicit none
- character :: c(mo_tot_num)
- integer :: i,k
-
- integer, allocatable :: occ(:,:,:), occ_tmp(:,:)
- !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: occ, occ_tmp
-
- call ezfio_set_determinants_det_num(N_det)
- call ezfio_set_determinants_det_coef(psi_coef_sorted(1,1))
-
- allocate (occ(elec_alpha_num,N_det,2))
- ! OMP PARALLEL DEFAULT(NONE) &
- ! OMP PRIVATE(occ_tmp,i,k)&
- ! OMP SHARED(N_det,psi_det_sorted,elec_alpha_num, &
- ! OMP   occ,elec_beta_num,N_int)
- allocate (occ_tmp(N_int*bit_kind_size,2))
- occ_tmp = 0
- ! OMP DO 
- do i=1,N_det
-  call bitstring_to_list(psi_det_sorted(1,1,i), occ_tmp(1,1), elec_alpha_num, N_int )
-  call bitstring_to_list(psi_det_sorted(1,2,i), occ_tmp(1,2), elec_beta_num, N_int )
-  do k=1,elec_alpha_num
-    occ(k,i,1) = occ_tmp(k,1)
-    occ(k,i,2) = occ_tmp(k,2)
-  enddo
- enddo
- ! OMP END DO
- deallocate(occ_tmp)
- ! OMP END PARALLEL
- call ezfio_set_determinants_det_occ(occ)
- call write_int(output_determinants,N_det,'Determinants saved for QMC')
- deallocate(occ)
- open(unit=31,file=trim(ezfio_filename)//'/mo_basis/mo_classif')
- write(31,'(I1)') 1
- write(31,*) mo_tot_num
- do i=1,mo_tot_num
-   write(31,'(A)') 'a'
- enddo
- close(31)
- call system('gzip -f '//trim(ezfio_filename)//'/mo_basis/mo_classif')
-
-end
-
-program save_for_qmc
- read_wf = .True.
- TOUCH read_wf
-!  call save_dets_qmcchem
- call write_spindeterminants
-end

src/Electrons/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-Output
+Ezfio_files

src/Electrons/README.rst

@@ -24,7 +24,9 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+.. image:: tree_dependancy.png
+
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 
 Documentation
 =============

src/Ezfio_files/README.rst

@@ -28,6 +28,24 @@ Documentation
   'x' : READ/WRITE, FORMATTED
   .br
 
+`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
+  Initial CPU and wall times when printing in the output files
+
+`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L1>`_
+  Initial CPU and wall times when printing in the output files
+
+`write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L88>`_
+  Write an logical value in output
+
+`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L58>`_
+  Write a double precision value in output
+
+`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L73>`_
+  Write an integer value in output
+
+`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L42>`_
+  Write a time stamp in the output for chronological reconstruction
+
 
 
 

src/Ezfio_files/output.irp.f

@@ -20,8 +20,8 @@ BEGIN_SHELL [ /bin/bash ]
   ! Output file for $NAME
   END_DOC
   PROVIDE output_wall_time_0 output_cpu_time_0 ezfio_filename
-  integer                        :: getUnitAndOpen
+!  integer                        :: getUnitAndOpen
-  call ezfio_set_output_empty(.False.)
+!  call ezfio_set_output_empty(.False.)
 IRP_IF COARRAY
   if (this_image() == 1) then
     output_$NAME = 6 !getUnitAndOpen(trim(ezfio_filename)//'/output/'//'$NAME.rst','a')

src/FCIdump/README.rst

@@ -10,9 +10,6 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/FCIdump/fcidump.irp.f#L1>`_
-  Undocumented
-
 
 
 Needed Modules
@@ -21,5 +18,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

src/Full_CI/EZFIO.cfg

@@ -1,35 +1,3 @@
-[N_det_max_fci]
-type: Det_number_max
-doc: Max number of determinants in the wave function
-interface: input
-default: 10000
-
-[N_det_max_fci_property]
-type: Det_number_max
-doc: Max number of determinants in the wave function when you select for a given property
-interface: input
-default: 10000
-
-[do_pt2_end]
-type: logical
-doc: If true, compute the PT2 at the end of the selection
-interface: input
-default: True
-
-[PT2_max]
-type: PT2_energy
-doc: The selection process stops when the largest PT2 (for all the state) is lower
-     than pt2_max in absolute value
-interface: input
-default: 0.0001
-
-[var_pt2_ratio]
-type: Normalized_float
-doc: The selection process stops when the energy ratio variational/(variational+PT2)
-     is equal to var_pt2_ratio
-interface: input
-default: 0.75
-
 [energy]
 type: double precision
 doc: Calculated Selected FCI energy

src/Full_CI/README.rst

@@ -24,6 +24,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_

src/Full_CI/full_ci.irp.f

@@ -11,12 +11,12 @@ program full_ci
   
   pt2 = 1.d0
   diag_algorithm = "Lapack"
-  if (N_det > n_det_max_fci) then
+  if (N_det > N_det_max) then
     call diagonalize_CI
     call save_wavefunction
     psi_det = psi_det_sorted
     psi_coef = psi_coef_sorted
-    N_det = n_det_max_fci
+    N_det = N_det_max
     soft_touch N_det psi_det psi_coef
     call diagonalize_CI
     call save_wavefunction
@@ -38,7 +38,7 @@ program full_ci
 
   integer :: n_det_before
   print*,'Beginning the selection ...'
-  do while (N_det < n_det_max_fci.and.maxval(abs(pt2(1:N_st))) > pt2_max)
+  do while (N_det < N_det_max.and.maxval(abs(pt2(1:N_st))) > pt2_max)
     n_det_before = N_det
     call H_apply_FCI(pt2, norm_pert, H_pert_diag,  N_st)
 
@@ -46,10 +46,10 @@ program full_ci
     PROVIDE  psi_det
     PROVIDE  psi_det_sorted
 
-    if (N_det > n_det_max_fci) then
+    if (N_det > N_det_max) then
        psi_det = psi_det_sorted
        psi_coef = psi_coef_sorted
-       N_det = n_det_max_fci
+       N_det = N_det_max
        soft_touch N_det psi_det psi_coef
     endif
     call diagonalize_CI
@@ -68,7 +68,7 @@ program full_ci
       exit
     endif
   enddo
-   N_det = min(n_det_max_fci,N_det)
+   N_det = min(N_det_max,N_det)
    touch N_det psi_det psi_coef
    call diagonalize_CI
    if(do_pt2_end)then

src/Full_CI/full_ci_no_skip.irp.f

@@ -11,12 +11,12 @@ program full_ci
   
   pt2 = 1.d0
   diag_algorithm = "Lapack"
-  if (N_det > n_det_max_fci) then
+  if (N_det > N_det_max) then
     call diagonalize_CI
     call save_wavefunction
     psi_det = psi_det_sorted
     psi_coef = psi_coef_sorted
-    N_det = n_det_max_fci
+    N_det = N_det_max
     soft_touch N_det psi_det psi_coef
     call diagonalize_CI
     call save_wavefunction
@@ -38,7 +38,7 @@ program full_ci
 
   integer :: n_det_before
   print*,'Beginning the selection ...'
-  do while (N_det < n_det_max_fci.and.maxval(abs(pt2(1:N_st))) > pt2_max)
+  do while (N_det < N_det_max.and.maxval(abs(pt2(1:N_st))) > pt2_max)
     n_det_before = N_det
     call H_apply_FCI_no_skip(pt2, norm_pert, H_pert_diag,  N_st)
 
@@ -46,10 +46,10 @@ program full_ci
     PROVIDE  psi_det
     PROVIDE  psi_det_sorted
 
-    if (N_det > n_det_max_fci) then
+    if (N_det > N_det_max) then
        psi_det = psi_det_sorted
        psi_coef = psi_coef_sorted
-       N_det = n_det_max_fci
+       N_det = N_det_max
        soft_touch N_det psi_det psi_coef
     endif
     call diagonalize_CI
@@ -68,7 +68,7 @@ program full_ci
       exit
     endif
   enddo
-   N_det = min(n_det_max_fci,N_det)
+   N_det = min(N_det_max,N_det)
    touch N_det psi_det psi_coef
    call diagonalize_CI
    if(do_pt2_end)then

src/Generators_CAS/README.rst

@@ -43,5 +43,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

src/Generators_full/README.rst

@@ -40,6 +40,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+.. image:: tree_dependancy.png
+
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
 

src/Hartree_Fock/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-Bielec_integrals MOGuess
+Integrals_Bielec MOGuess

src/Hartree_Fock/README.rst

@@ -10,7 +10,9 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+.. image:: tree_dependancy.png
+
+* `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
 * `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 
 Documentation

src/Integrals_Bielec/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Pseudo MOs Bitmask

src/Integrals_Bielec/README.rst

@@ -16,7 +16,10 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+.. image:: tree_dependancy.png
+
+* `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 
 Documentation
@@ -25,192 +28,192 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1>`_
+`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1>`_
   integral of the AO basis <ik|jl> or (ij|kl)
   i(r1) j(r1) 1/r12 k(r2) l(r2)
 
-`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L491>`_
+`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L489>`_
   Needed to compute Schwartz inequalities
 
-`ao_bielec_integral_schwartz_accel <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L107>`_
+`ao_bielec_integral_schwartz_accel <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L107>`_
   integral of the AO basis <ik|jl> or (ij|kl)
   i(r1) j(r1) 1/r12 k(r2) l(r2)
 
-`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L322>`_
+`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L322>`_
   Map of Atomic integrals
   i(r1) j(r2) 1/r12 k(r1) l(r2)
 
-`ao_l4 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L279>`_
+`ao_l4 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L279>`_
   Computes the product of l values of i,j,k,and l
 
-`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L290>`_
+`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L290>`_
   Compute AO 1/r12 integrals for all i and fixed j,k,l
 
-`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L654>`_
+`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L652>`_
   ATOMIC PRIMTIVE bielectronic integral between the 4 primitives ::
   primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
   primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2)
   primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
   primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)
 
-`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L516>`_
+`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L514>`_
   Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
 
-`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L852>`_
+`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L850>`_
   subroutine that returns the explicit polynom in term of the "t"
   variable of the following polynomw :
   I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
 
-`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L773>`_
+`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L771>`_
   recursive function involved in the bielectronic integral
 
-`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L915>`_
+`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L913>`_
   recursive function involved in the bielectronic integral
 
-`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1035>`_
+`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1033>`_
   recursive function involved in the bielectronic integral
 
-`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1089>`_
+`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1087>`_
   recursive function involved in the bielectronic integral
 
-`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L949>`_
+`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L947>`_
   recursive function involved in the bielectronic integral
 
-`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L808>`_
+`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L806>`_
   recursive function involved in the bielectronic integral
 
-`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1151>`_
+`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1149>`_
   recursive function involved in the bielectronic integral
 
-`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L699>`_
+`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L697>`_
   calculate the integral of the polynom ::
   I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
   between ( 0 ; 1)
 
-`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L838>`_
+`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L836>`_
   Returns the upper boundary of the degree of the polynomial involved in the
   bielctronic integral :
   Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)
 
-`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L29>`_
+`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L29>`_
   Gauss-Legendre
 
-`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L10>`_
+`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L10>`_
   t_w(i,1,k) = w(i)
   t_w(i,2,k) = t(i)
 
-`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L11>`_
+`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L11>`_
   t_w(i,1,k) = w(i)
   t_w(i,2,k) = t(i)
 
-`n_pt_max_integrals_16 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L1>`_
+`n_pt_max_integrals_16 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/gauss_legendre.irp.f#L1>`_
   Aligned n_pt_max_integrals
 
-`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L6>`_
+`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L6>`_
   AO integrals
 
-`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L19>`_
+`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L19>`_
   Undocumented
 
-`bielec_integrals_index_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L36>`_
+`bielec_integrals_index_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L36>`_
   Undocumented
 
-`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L223>`_
+`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L223>`_
   Frees the memory of the AO map
 
-`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L399>`_
+`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L399>`_
   Frees the memory of the MO map
 
-`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L113>`_
+`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L113>`_
   Gets one AO bi-electronic integral from the AO map
 
-`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L137>`_
+`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L137>`_
   Gets multiple AO bi-electronic integral from the AO map .
   All i are retrieved for j,k,l fixed.
 
-`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L172>`_
+`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L172>`_
   Gets multiple AO bi-electronic integral from the AO map .
   All non-zero i are retrieved for j,k,l fixed.
 
-`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L214>`_
+`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L214>`_
   Returns the number of elements in the AO map
 
-`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L281>`_
+`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L281>`_
   Returns one integral <ij|kl> in the MO basis
 
-`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L310>`_
+`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L310>`_
   Returns multiple integrals <ij|kl> in the MO basis, all
   i for j,k,l fixed.
 
-`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L341>`_
+`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L341>`_
   Returns multiple integrals <ij|kl> in the MO basis, all
   i(1)j(1) 1/r12 k(2)l(2)
   i for j,k,l fixed.
 
-`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L391>`_
+`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L391>`_
   Return the number of elements in the MO map
 
-`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L250>`_
+`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L250>`_
   Create new entry into AO map
 
-`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L265>`_
+`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L265>`_
   Create new entry into MO map, or accumulate in an existing entry
 
-`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L298>`_
+`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L298>`_
   Returns one integral <ij|kl> in the MO basis
 
-`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L237>`_
+`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L237>`_
   MO integrals
 
-`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L42>`_
+`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L42>`_
   Adds integrals to tha MO map according to some bitmask
 
-`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L465>`_
+`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L465>`_
   mo_bielec_integral_jj(i,j) = J_ij
   mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
-`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L467>`_
+`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L467>`_
   mo_bielec_integral_jj(i,j) = J_ij
   mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
-`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L327>`_
+`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L327>`_
   mo_bielec_integral_jj_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
 
-`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L466>`_
+`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L466>`_
   mo_bielec_integral_jj(i,j) = J_ij
   mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
-`mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L326>`_
+`mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L326>`_
   mo_bielec_integral_jj_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
 
-`mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L325>`_
+`mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L325>`_
   mo_bielec_integral_jj_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
   mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
 
-`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L22>`_
+`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L22>`_
   If True, the map of MO bielectronic integrals is provided
 
-`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L1>`_
+`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L1>`_
   Computes an unique index for i,j,k,l integrals
 
-`read_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L1>`_
+`read_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/read_write.irp.f#L1>`_
   One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
 
-`read_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L2>`_
+`read_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/read_write.irp.f#L2>`_
   One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
 
-`write_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L3>`_
+`write_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/read_write.irp.f#L3>`_
   One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
 
-`write_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L4>`_
+`write_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/read_write.irp.f#L4>`_
   One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
 
 

src/Integrals_Bielec/ao_bi_integrals.irp.f

@@ -349,7 +349,7 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
     integer                        :: load_ao_integrals
     print*,'Reading the AO integrals'
     if (load_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin') == 0) then
-      write(output_bielec_integrals,*) 'AO integrals provided'
+      print*, 'AO integrals provided'
       ao_bielec_integrals_in_map = .True.
       return
     endif
@@ -367,7 +367,7 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
   PROVIDE progress_bar
   call omp_init_lock(lock)
   lmax = ao_num*(ao_num+1)/2
-  write(output_bielec_integrals,*) 'Providing the AO integrals'
+  print*, 'Providing the AO integrals'
   call wall_time(wall_0)
   call wall_time(wall_1)
   call cpu_time(cpu_1)
@@ -378,7 +378,7 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
       !$OMP DEFAULT(NONE)                                            &
       !$OMP SHARED (ao_num, jl_pairs, ao_integrals_map,thresh,       &
       !$OMP    cpu_1,wall_1,lock, lmax,n_centers,ao_nucl,            &
-      !$OMP    ao_overlap_abs,ao_overlap,output_bielec_integrals,abort_here,   &
+      !$OMP    ao_overlap_abs,ao_overlap,abort_here,   &
       !$OMP    wall_0,progress_bar,progress_value)
   
   allocate(buffer_i(size_buffer))
@@ -445,7 +445,7 @@ IRP_ENDIF
     if (thread_num == 0) then
       if (wall_2 - wall_0 > 1.d0) then
         wall_0 = wall_2
-        write(output_bielec_integrals,*) 100.*float(kk)/float(lmax), '% in ',  &
+        print*, 100.*float(kk)/float(lmax), '% in ',  &
             wall_2-wall_1, 's', map_mb(ao_integrals_map) ,'MB'
         progress_value = dble(map_mb(ao_integrals_map))
       endif
@@ -462,32 +462,30 @@ IRP_ENDIF
     stop 'Aborting in AO integrals calculation'
   endif
 IRP_IF COARRAY
-  write(output_bielec_integrals,*) 'Communicating the map'
+  print*, 'Communicating the map'
   call communicate_ao_integrals()
 IRP_ENDIF COARRAY
-  write(output_bielec_integrals,*) 'Sorting the map'
+  print*, 'Sorting the map'
   call map_sort(ao_integrals_map)
   call cpu_time(cpu_2)
   call wall_time(wall_2)
   integer(map_size_kind)         :: get_ao_map_size, ao_map_size
   ao_map_size = get_ao_map_size()
   
-  write(output_bielec_integrals,*) 'AO integrals provided:'
+  print*, 'AO integrals provided:'
-  write(output_bielec_integrals,*) ' Size of AO map :         ', map_mb(ao_integrals_map) ,'MB'
+  print*, ' Size of AO map :         ', map_mb(ao_integrals_map) ,'MB'
-  write(output_bielec_integrals,*) ' Number of AO integrals :', ao_map_size
+  print*, ' Number of AO integrals :', ao_map_size
-  write(output_bielec_integrals,*) ' cpu  time :',cpu_2 - cpu_1, 's'
+  print*, ' cpu  time :',cpu_2 - cpu_1, 's'
-  write(output_bielec_integrals,*) ' wall time :',wall_2 - wall_1, 's  ( x ', (cpu_2-cpu_1)/(wall_2-wall_1+tiny(1.d0)), ' )'
+  print*, ' wall time :',wall_2 - wall_1, 's  ( x ', (cpu_2-cpu_1)/(wall_2-wall_1+tiny(1.d0)), ' )'
   
   ao_bielec_integrals_in_map = .True.
   if (write_ao_integrals) then
     call dump_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin')
-    call ezfio_set_bielec_integrals_disk_access_ao_integrals(.True.)
+    call ezfio_set_integrals_bielec_disk_access_ao_integrals(.True.)
   endif
   
 END_PROVIDER
  
-
-
 BEGIN_PROVIDER [ double precision, ao_bielec_integral_schwartz,(ao_num,ao_num)  ]
   implicit none
   BEGIN_DOC

src/Integrals_Bielec/map_integrals.irp.f

@@ -13,7 +13,7 @@ BEGIN_PROVIDER [ type(map_type), ao_integrals_map ]
   call bielec_integrals_index(ao_num,ao_num,ao_num,ao_num,key_max)
   sze = key_max
   call map_init(ao_integrals_map,sze)
-  write(output_bielec_integrals,*)  'AO map initialized'
+  print*,  'AO map initialized'
 END_PROVIDER
 
 subroutine bielec_integrals_index(i,j,k,l,i1)
@@ -244,7 +244,7 @@ BEGIN_PROVIDER [ type(map_type), mo_integrals_map ]
   call bielec_integrals_index(mo_tot_num,mo_tot_num,mo_tot_num,mo_tot_num,key_max)
   sze = key_max
   call map_init(mo_integrals_map,sze)
-  write(output_bielec_integrals,*) 'MO map initialized'
+  print*, 'MO map initialized'
 END_PROVIDER
 
 subroutine insert_into_ao_integrals_map(n_integrals,                 &

src/Integrals_Bielec/mo_bi_integrals.irp.f

@@ -31,7 +31,7 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ]
     integer                        :: load_mo_integrals
     print*,'Reading the MO integrals'
     if (load_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin') == 0) then
-      write(output_bielec_integrals,*) 'MO integrals provided'
+      print*, 'MO integrals provided'
       return
     endif
   endif
@@ -84,8 +84,8 @@ subroutine add_integrals_to_map(mask_ijkl)
   call bitstring_to_list( mask_ijkl(1,4), list_ijkl(1,4), n_l, N_int )
   
   size_buffer = min(ao_num*ao_num*ao_num,16000000)
-  write(output_bielec_integrals,*) 'Providing the molecular integrals '
+  print*, 'Providing the molecular integrals '
-  write(output_bielec_integrals,*) 'Buffers : ', 8.*(mo_tot_num_align*(n_j)*(n_k+1) + mo_tot_num_align +&
+  print*, 'Buffers : ', 8.*(mo_tot_num_align*(n_j)*(n_k+1) + mo_tot_num_align +&
       ao_num+ao_num*ao_num+ size_buffer*3)/(1024*1024), 'MB / core'
   
   call wall_time(wall_1)
@@ -99,7 +99,7 @@ subroutine add_integrals_to_map(mask_ijkl)
       !$OMP  wall_0,thread_num)   &
       !$OMP  DEFAULT(NONE)                                           &
       !$OMP  SHARED(size_buffer,ao_num,mo_tot_num,n_i,n_j,n_k,n_l,mo_tot_num_align,&
-      !$OMP  mo_coef_transp,output_bielec_integrals,                           &
+      !$OMP  mo_coef_transp,                                         &
       !$OMP  mo_coef_transp_is_built, list_ijkl,                     &
       !$OMP  mo_coef_is_built, wall_1, abort_here,                   &
       !$OMP  mo_coef,mo_integrals_threshold,ao_integrals_map,mo_integrals_map,progress_bar,progress_value)
@@ -272,7 +272,7 @@ IRP_ENDIF
     if (thread_num == 0) then
       if (wall_2 - wall_0 > 1.d0) then
         wall_0 = wall_2
-        write(output_bielec_integrals,*) 100.*float(l1)/float(ao_num), '% in ',  &
+        print*, 100.*float(l1)/float(ao_num), '% in ',  &
             wall_2-wall_1, 's', map_mb(mo_integrals_map) ,'MB'
         progress_value = dble(map_mb(mo_integrals_map))
 
@@ -291,7 +291,7 @@ IRP_ENDIF
     stop 'Aborting in MO integrals calculation'
   endif
 IRP_IF COARRAY
-  write(output_bielec_integrals,*) 'Communicating the map'
+  print*, 'Communicating the map'
   call communicate_mo_integrals()
 IRP_ENDIF
   call map_unique(mo_integrals_map)
@@ -304,15 +304,15 @@ IRP_ENDIF
   deallocate(list_ijkl)
   
   
-  write(output_bielec_integrals,*)'Molecular integrals provided:'
+  print*,'Molecular integrals provided:'
-  write(output_bielec_integrals,*)' Size of MO map           ', map_mb(mo_integrals_map) ,'MB'
+  print*,' Size of MO map           ', map_mb(mo_integrals_map) ,'MB'
-  write(output_bielec_integrals,*)' Number of MO integrals: ',  mo_map_size
+  print*,' Number of MO integrals: ',  mo_map_size
-  write(output_bielec_integrals,*)' cpu  time :',cpu_2 - cpu_1, 's'
+  print*,' cpu  time :',cpu_2 - cpu_1, 's'
-  write(output_bielec_integrals,*)' wall time :',wall_2 - wall_1, 's  ( x ', (cpu_2-cpu_1)/(wall_2-wall_1), ')'
+  print*,' wall time :',wall_2 - wall_1, 's  ( x ', (cpu_2-cpu_1)/(wall_2-wall_1), ')'
   
   if (write_mo_integrals) then
     call dump_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin')
-    call ezfio_set_bielec_integrals_disk_access_mo_integrals(.True.)
+    call ezfio_set_integrals_bielec_disk_access_mo_integrals(.True.)
   endif
   
   

src/Integrals_Monoelec/Makefile

@@ -0,0 +1,6 @@
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=pseudopot.f90
+OBJ=IRPF90_temp/pseudopot.o
+
+include $(QPACKAGE_ROOT)/src/Makefile.common

src/Integrals_Monoelec/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+MOs Pseudo