Merge pull request #35 from scemama/master

Introduce ezfio_interface.py and EZFIO.cfg in Full_CI

.gitignore

@@ -1,3 +1,8 @@
 quantum_package.rc
 EZFIO
 irpf90
+EMSL_Basis
+bin/
+*.log
+quantum_package_static.tar.gz
+

ocaml/Makefile

@@ -13,7 +13,7 @@ endif
 LIBS=
 PKGS=
 OCAMLCFLAGS="-g -warn-error A"
-OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) -ocamlopt ocamlc.opt
+OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) 
 MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
 MLIFILES=$(wildcard *.mli) 
 ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))

scripts/ezfio_interface.py

@@ -0,0 +1,268 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Take a path in argv
+Check if EZFIO.cfg exists.
+EZFIO.cfg are in MODULE directories.
+create : ezfio_interface.irp.f
+         folder_ezfio_inteface_config
+
+Example EZFIO.cfg:
+```
+[thresh_SCF]
+doc: Threshold on the convergence of the Hartree Fock energy
+type: Threshold
+default: 1.e-10
+
+[do_pt2_end]
+type: logical
+doc: If true, compute the PT2 at the end of the selection
+default: true
+```
+
+"""
+
+import sys
+import os
+import os.path
+
+import ConfigParser
+
+from collections import defaultdict
+from collections import namedtuple
+
+Type = namedtuple('Type', 'ocaml fortran')
+def bool_convertor(b):
+  return ( b.lower() in [ "true", ".true." ] )
+
+
+def get_type_dict():
+    """
+    This function makes the correspondance between the type of value read in
+    ezfio.cfg into the f90 and Ocam Type
+    return fancy_type[fancy_type] = namedtuple('Type', 'ocaml fortran')
+    For example fancy_type['Ndet'].fortran = interger
+                                  .ocaml   = int
+    """
+
+    # ~#~#~#~ #
+    # I n i t #
+    # ~#~#~#~ #
+
+    # Dict to change ocaml LowLevel type into FortranLowLevel type
+    ocaml_to_fortran = {"int": "integer",
+                        "float": "double precision",
+                        "logical": "logical",
+                        "string": "character*60"}
+
+    fancy_type = defaultdict(dict)
+
+    # ~#~#~#~#~#~#~#~ #
+    # R a w _ t y p e #
+    # ~#~#~#~#~#~#~#~ #
+
+    fancy_type['integer'] = Type("int", "integer")
+    fancy_type['int'    ] = Type("int", "integer")
+
+    fancy_type['float'           ] = Type("float", "double precision")
+    fancy_type['double precision'] = Type("float", "double precision")
+
+    fancy_type['logical'] = Type("bool", "logical")
+    fancy_type['bool'   ] = Type("bool", "logical")
+
+    # ~#~#~#~#~#~#~#~ #
+    # q p _ t y p e s #
+    # ~#~#~#~#~#~#~#~ #
+
+    src = os.environ['QPACKAGE_ROOT'] + "/ocaml/qptypes_generator.ml"
+
+    with open(src, "r") as f:
+        l = [i for i in f.read().splitlines() if i.strip().startswith("*")]
+
+    for i in l:
+        ocaml_fancy_type = i.split()[1].strip()
+        ocaml_type = i.split()[3]
+        fortran_type = ocaml_to_fortran[ocaml_type]
+
+        fancy_type[ocaml_fancy_type] = Type(ocaml_type, fortran_type)
+
+    return dict(fancy_type)
+
+
+type_dict = get_type_dict()
+
+
+def get_dict_config_file(config_file_path,folder):
+    """
+    Read a ezfio.cfg
+    Return a dict d[provider_name] = {type, default, ezfio_name,ezfio_dir,doc}
+    """
+    # ~#~#~#~ #
+    # I n i t #
+    # ~#~#~#~ #
+
+    d = defaultdict(dict)
+    list_option_required = ["default", "doc"]
+    list_option          = ["ezfio_name", "output"]
+
+    # ~#~#~#~#~#~#~#~#~#~#~ #
+    # L o a d _ C o n f i g #
+    # ~#~#~#~#~#~#~#~#~#~#~ #
+
+    config_file = ConfigParser.ConfigParser()
+    config_file.readfp(open(config_file_path))
+
+    # ~#~#~#~#~#~#~#~#~ #
+    # F i l l _ d i c t #
+    # ~#~#~#~#~#~#~#~#~ #
+
+    provider_names = config_file.sections()
+    for p in provider_names:
+        provider_name = p.lower()
+        default_d = {"ezfio_name": provider_name, "output": "false" }
+        # Check if type if avalaible
+        type_ = config_file.get(p, "type")
+        if type_ not in type_dict:
+            print "{0} not avalaible. Choose in:".format(type_)
+            print ", ".join([i for i in type_dict])
+            sys.exit(1)
+        else:
+            d[provider_name]["type"] = type_dict[type_]
+
+        # Fill the dict with allother the information
+        for k in list_option_required:
+            try:
+                d[provider_name][k] = config_file.get(p, k)
+            except ConfigParser.NoOptionError:
+                print "You need a {0} for {1} in {2}".format(k,
+                                                             provider_name,
+                                                             config_file_path)
+        d[provider_name]["ezfio_dir"] = folder
+        for k in list_option:
+            try:
+                d[provider_name][k] = config_file.get(p, k).lower()
+            except ConfigParser.NoOptionError:
+                d[provider_name][k] = default_d[k]
+
+        # Convert string to bool
+        d[provider_name]["output"] = bool_convertor(d[provider_name]["output"])
+
+    return dict(d)
+
+
+def create_ezfio_provider(dict_ezfio_cfg):
+    """
+    From dict d[provider_name] = {type, default, ezfio_name,ezfio_dir,doc}
+    create the a list who containt all the code for the provider
+    return [code, ...]
+    """
+    from ezfio_with_default import EZFIO_Provider
+
+    dict_code_provider = dict()
+
+    ez_p = EZFIO_Provider()
+    for provider_name, dict_info in dict_ezfio_cfg.iteritems():
+        if not dict_info["output"]:
+            ez_p.set_type(dict_info['type'].fortran)
+            ez_p.set_name(provider_name)
+            ez_p.set_doc(dict_info['doc'])
+            ez_p.set_ezfio_dir(dict_info['ezfio_dir'])
+            ez_p.set_ezfio_name(dict_info['ezfio_name'])
+            ez_p.set_default(dict_info['default'])
+     
+            ez_p.set_output("output_%s" % dict_info['ezfio_dir'])
+            dict_code_provider[provider_name] = str(ez_p)
+
+    return dict_code_provider
+
+
+def save_ezfio_provider(path_head, dict_code_provider):
+    """
+    Write in "ezfio_interface.irp.f" the
+    value of dict_code_provider
+    """
+
+    path = "{0}/ezfio_interface.irp.f".format(path_head)
+
+    print "Path = {}".format(path)
+
+    with open(path, "w") as f:
+        f.write("!DO NOT MODIFY BY HAND \n")
+        f.write("!Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py \n")
+        f.write("!from file {0}/EZFIO.cfg\n".format(path_head))
+        f.write("\n")
+        for provider_name, code in dict_code_provider.iteritems():
+            f.write(code + "\n")
+
+
+def create_ezfio_config(dict_ezfio_cfg, opt, folder):
+    """
+    From dict_ezfio_cfg[provider_name] = {type, default, ezfio_name,ezfio_dir,doc}
+    Return the string ezfio_interface_config
+    """
+
+    result = [ folder ]
+    lenmax = max( [ len(i) for i in dict_ezfio_cfg ]  )+2
+    l = sorted(dict_ezfio_cfg.keys())
+    for provider_name in l:
+      provider_info = dict_ezfio_cfg[provider_name]
+      s = "  {0} {1}".format( provider_name.lower().ljust(lenmax), provider_info["type"].fortran )
+      result.append(s)
+    return "\n".join(result)
+
+def save_ezfio_config(folder, str_ezfio_config):
+    """
+    Write the str_ezfio_config in
+    $QPACKAGE_ROOT/EZFIO/{0}.ezfio_interface_config".format(folder)
+    """
+
+    ezfio_dir = "{0}/EZFIO".format(os.environ['QPACKAGE_ROOT'])
+    path = "{0}/config/{1}.ezfio_interface_config".format(ezfio_dir,
+                                                          folder)
+
+    print "Path = {}".format(path)
+
+    with open(path, "w") as f:
+        f.write(str_ezfio_config)
+
+def main():
+    """Take in argument a EZFIO.cfg"""
+
+    try:
+      path = sys.argv[1]
+    except:
+      path = "EZFIO.cfg"
+      if "EZFIO.cfg" not in os.listdir(os.getcwd()):
+        sys.exit(0)
+
+    path = os.path.expanduser(path)
+    path = os.path.expandvars(path)
+    path = os.path.abspath(path)
+    print path
+
+    path_dirname = os.path.dirname(path)
+    folder = [i for i in path_dirname.split("/") if i][-1]
+    folder = folder.lower()
+
+    print "Find a EZFIO.cfg in {}".format(path)
+    dict_info_provider = get_dict_config_file(path,folder)
+
+    print "Generating the ezfio_interface.irp.f: \n"
+    d_config = create_ezfio_provider(dict_info_provider)
+#    for provider, code in d_config.iteritems():
+#        print code
+
+    print "Saving the ezfio_interface.irp.f"
+    save_ezfio_provider(path_dirname, d_config)
+
+    print "Generating the ezfio_config"
+    config_ezfio = create_ezfio_config(dict_info_provider, "config", folder)
+#    print config_ezfio
+
+    print "Saving ezfio_config"
+    save_ezfio_config(folder, config_ezfio)
+
+
+if __name__ == "__main__":
+  main()
+

src/.gitignore

@@ -1 +1,2 @@
 Makefile.config
+ezfio_interface.irp.f

src/CAS_SD_selected/README.rst

@@ -0,0 +1,5 @@
+======================
+CAS_SD_selected Module
+======================
+
+Selected CAS + SD module

src/Full_CI/EZFIO.cfg

@@ -0,0 +1,37 @@
+[N_det_max_fci]
+doc: Max number of determinants in the wave function
+type: Det_number_max
+default: 10000
+
+[N_det_max_fci_property]
+doc: Max number of determinants in the wave function when you select for a given property
+type: Det_number_max
+default: 10000
+
+[do_pt2_end]
+type: logical
+doc: If true, compute the PT2 at the end of the selection
+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
+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
+default: 0.75
+
+[energy]
+type: double precision
+doc: "Calculated Full CI energy"
+output: true
+
+[energy_pt2]
+type: double precision
+doc: "Calculated Full CI energy"
+output: true
+

src/Full_CI/full_ci.ezfio_config

@@ -1,8 +0,0 @@
-full_ci
-  n_det_max_fci           integer 
-  n_det_max_fci_property  integer 
-  pt2_max                 double precision
-  do_pt2_end              logical
-  energy                  double precision
-  energy_pt2              double precision
-  var_pt2_ratio           double precision

src/Full_CI/options.irp.f

@@ -1,41 +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      ( "integer" )
-T.set_name      ( "N_det_max_fci_property" )
-T.set_doc       ( "Max number of determinants in the wave function when you select for a given property" )
-T.set_ezfio_dir ( "full_ci" )
-T.set_ezfio_name( "N_det_max_fci_property" )
-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/Full_CI/target_pt2.irp.f

@@ -0,0 +1,76 @@
+program var_pt2_ratio_run
+  implicit none
+  integer                        :: i,k
+
+  
+  double precision, allocatable  :: pt2(:), norm_pert(:), H_pert_diag(:)
+  integer                        :: N_st, degree
+  N_st = N_states
+  allocate (pt2(N_st), norm_pert(N_st),H_pert_diag(N_st))
+  character*(64)                 :: perturbation
+  
+  double precision, allocatable  :: psi_det_save(:,:,:), psi_coef_save(:,:)
+
+  double precision :: E_fci, E_var, ratio, E_ref
+  integer :: Nmin, Nmax
+
+  pt2 = -(pt2_max+1.d0)
+  diag_algorithm = "Lapack"
+
+  ratio = 0.d0
+  Nmin=1
+  do while (dabs(pt2(1)) > pt2_max)
+    call H_apply_FCI(pt2, norm_pert, H_pert_diag,  N_st)
+    psi_det = psi_det_sorted
+    psi_coef = psi_coef_sorted
+    soft_touch N_det psi_det psi_coef
+    call diagonalize_CI
+    ratio = (CI_energy(1) - HF_energy) / (CI_energy(1)+pt2(1) - HF_energy)
+  enddo
+
+  threshold_selectors = 1.d0
+  threshold_generators = 0.999d0
+  call diagonalize_CI
+  call H_apply_FCI_PT2(pt2, norm_pert, H_pert_diag,  N_st)
+  E_ref = CI_energy(1) + pt2(1)
+  threshold_selectors = 0.99d0
+  threshold_generators = 0.98d0
+   
+  var_pt2_ratio = (E_ref + pt2_max - HF_energy) / (E_ref - HF_energy)
+  TOUCH var_pt2_ratio
+
+  Nmax=max(10000,3*N_det)
+  Nmin=1
+  do while (Nmax-Nmin > 1)
+    ratio = (CI_energy(1) - HF_energy) / (E_ref - HF_energy)
+
+    if (ratio < var_pt2_ratio) then
+      Nmin = N_det
+!      Nmax = max(Nmax,Nmin+10)
+      ! Select new determinants
+      call H_apply_FCI(pt2, norm_pert, H_pert_diag,  N_st)
+      N_det = min(N_det,Nmax)
+    else
+      Nmax = N_det
+      N_det = Nmin + (Nmax-Nmin)/2
+    endif
+
+    psi_det = psi_det_sorted
+    psi_coef = psi_coef_sorted
+    soft_touch N_det psi_det psi_coef
+    call diagonalize_CI
+    call save_wavefunction
+    print *,  'Det min, Det max: ', Nmin, Nmax
+    print *,  'Ratio           : ', ratio, '  ~  ', var_pt2_ratio
+    print *,  'HF_energy = ', HF_energy
+    print *,  'Est FCI   = ', E_ref
+    print *,  'PT2       = ', pt2(1)
+    print *,  'N_det     = ', N_det
+    print *,  'E         = ', CI_energy(1)
+    call ezfio_set_full_ci_energy(CI_energy)
+    if (abort_all) then
+      exit
+    endif
+  enddo
+  deallocate(pt2,norm_pert)
+end

src/Makefile.common

@@ -15,8 +15,8 @@ $(info  -------------------- Error --------------------)
 $(info  QPACKAGE_ROOT undefined. Run the setup_environment.sh script)
 $(info  -----------------------------------------------)
 $(error )
-else
-$(info  QPACKAGE_ROOT is defined.)
+#else
+#$(info  QPACKAGE_ROOT is defined.)
 endif
 
 
@@ -30,8 +30,8 @@ $(info You can create Makefile.config)
 $(info by modifying Makefile.config.example)
 $(info  -----------------------------------------------)
 $(error )
-else
-$(info  Makefile.config is present.)
+#else
+#$(info  Makefile.config is present.)
 endif
 
 
@@ -50,8 +50,8 @@ $(info  To upgrade IRPF90, run :                       )
 $(info    $(QPACKAGE_ROOT)/scripts/upgrade_irpf90.sh   )
 $(info  -----------------------------------------------)
 $(error )
-else
-$(info  irpf90 version is OK.)
+#else
+#$(info  irpf90 version is OK.)
 endif
 
 
@@ -69,8 +69,8 @@ $(info Your NEEDED_MODULES file is inconsistent. It should be)
 $(info $(NEEDED_MODULES_OK))
 $(info  -----------------------------------------------)
 $(error )
-else
-$(info  NEEDED_MODULES files is consistent.)
+#else
+#$(info  NEEDED_MODULES files is consistent.)
 endif
 
 
@@ -91,8 +91,8 @@ $(info  You should document it before you compile, as)
 $(info  well as the ASSUMPTIONS.rst file.)
 $(info  -----------------------------------------------)
 $(error )
-else
-$(info  README.rst is present.)
+#else
+#$(info  README.rst is present.)
 endif
 
 
@@ -104,8 +104,8 @@ $(info  -------------------- Error --------------------)
 $(info This is a Bug. At that point, the ASSUMPTIONS.rst)
 $(info file should exist.)
 $(info  -----------------------------------------------)
-else
-$(info  ASSUMPTIONS.rst is present.)
+#else
+#$(info  ASSUMPTIONS.rst is present.)
 endif
 
 
@@ -125,19 +125,27 @@ $(info  To upgrade EZFIO, run :                        )
 $(info    $(QPACKAGE_ROOT)/scripts/upgrade_ezfio.sh    )
 $(info  -----------------------------------------------)
 $(error )
-else
-$(info  EZFIO version is OK.)
+#else
+#$(info  EZFIO version is OK.)
 endif
 
 # Define the EZFIO rules
 
-$(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config)
+$(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg)
 	@echo Building EZFIO library
-	@cp $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(EZFIO_DIR)/config 
-	@cd $(EZFIO_DIR) ; export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ; $(MAKE) ; $(MAKE) Python
+	@echo =-=-=-=-=-=-=-=-=-=-=-
+	for dir in $(QPACKAGE_ROOT)/src/*/ ;\
+	do \
+	        cd $$dir && \
+		$(QPACKAGE_ROOT)/scripts/ezfio_interface.py && \
+		cd .. ;\
+	done
+	cp $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(EZFIO_DIR)/config 
+	cd $(EZFIO_DIR) ; export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ; $(MAKE) ; $(MAKE) Python
 
 ezfio: $(EZFIO)
 
+
 # Create symbolic links of other modules
 
 ifneq ($(PWD),$(QPACKAGE_ROOT)/src)

src/Properties/ASSUMPTIONS.rst

@@ -0,0 +1 @@
+THIS FILE HAS TO BE FILLED