Merge pull request #89 from TApplencourt/master

Fix ocaml makefile

configure

@@ -45,7 +45,7 @@ QP_ROOT = os.getcwd()
 QP_ROOT_BIN = join(QP_ROOT, "bin")
 QP_ROOT_INSTALL = join(QP_ROOT, "install")
 
-os.environ["PATH"] = os.environ["PATH"] + ":"+QP_ROOT_BIN
+os.environ["PATH"] = os.environ["PATH"] + ":" + QP_ROOT_BIN
 
 d_dependency = {
     "ocaml": ["m4", "curl", "zlib", "patch", "gcc"],
@@ -72,7 +72,8 @@ path_github = {"head": "http://github.com/", "tail": "archive/master.tar.gz"}
 
 ocaml = Info(
     url='http://raw.github.com/ocaml/opam/master/shell/opam_installer.sh',
-    description=' Ocaml, Opam and the Core library (it will take some time roughly 20min)',
+    description=
+    ' Ocaml, Opam and the Core library (it will take some time roughly 20min)',
     default_path=join(QP_ROOT_BIN, "opam"))
 
 m4 = Info(
@@ -133,7 +134,7 @@ for m in ["ocaml", "m4", "curl", "zlib", "path", "irpf90", "docopt",
     exec ("d_info['{0}']={0}".format(m))
 
 
-def find_path(bin_, l_installed):
+def find_path(bin_, l_installed, var_for_qp_root=False):
     """Use the global variable
     * l_installed
     * d_info
@@ -143,6 +144,10 @@ def find_path(bin_, l_installed):
         locate = l_installed[bin_]
     except KeyError:
         locate = d_info[bin_].default_path
+
+    if var_for_qp_root:
+        locate = locate.replace(QP_ROOT, "${QP_ROOT}")
+
     return locate
 
 
@@ -158,7 +163,8 @@ def check_output(*popenargs, **kwargs):
     >>> check_output(['/usr/bin/python', '--version'])
     Python 2.6.2
     """
-    process = subprocess.Popen(stdout=subprocess.PIPE,stderr=subprocess.PIPE, *popenargs, **kwargs)
+    process = subprocess.Popen(stdout=subprocess.PIPE,
+                               stderr=subprocess.PIPE, *popenargs, **kwargs)
     output, unused_err = process.communicate()
     retcode = process.poll()
     if retcode:
@@ -277,7 +283,8 @@ def installation(l_install_descendant):
     def create_rule_ninja():
 
         l_rules = [
-            "rule download", "  command = wget --no-check-certificate ${url} -O ${out} -o /dev/null",
+            "rule download",
+            "  command = wget --no-check-certificate ${url} -O ${out} -o /dev/null",
             "  description = Downloading ${descr}", ""
         ]
 
@@ -429,12 +436,15 @@ def create_ninja_and_rc(l_installed):
             if os.path.isdir(path):
                 l_python.append(path)
 
-    l_rc = [ 'export QP_ROOT={0}'.format(QP_ROOT) ] + \
+    path_ezfio = find_path('ezfio', l_installed, var_for_qp_root=True)
-       [ i.replace(QP_ROOT,"${QP_ROOT}") for i in 
+    path_irpf90 = find_path("irpf90", l_installed, var_for_qp_root=True)
-       [ 
+    path_ninja = find_path("ninja", l_installed, var_for_qp_root=True)
-        'export QP_EZFIO={0}'.format(find_path('ezfio', l_installed)),
+
-        'export IRPF90={0}'.format(find_path("irpf90", l_installed)),
+    l_rc = [
-        'export NINJA={0}'.format(find_path("ninja", l_installed)),
+        'export QP_ROOT={0}'.format(QP_ROOT),
+        'export QP_EZFIO={0}'.format(path_ezfio),
+        'export IRPF90={0}'.format(path_irpf90),
+        'export NINJA={0}'.format(path_ninja),
         'export QP_PYTHON={0}'.format(":".join(l_python)), "",
         'export PYTHONPATH="${QP_PYTHON}":"${PYTHONPATH}"',
         'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"',
@@ -443,7 +453,7 @@ def create_ninja_and_rc(l_installed):
         'source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh', "",
         'source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true',
         ""
-      ] ]
+    ]
 
     path = join(QP_ROOT, "quantum_package.rc")
     with open(path, "w+") as f:
@@ -451,16 +461,14 @@ def create_ninja_and_rc(l_installed):
 
     print "[  OK  ] ({0})".format(path)
 
-    print str_info("build"),
-
     command = ['bash', '-c', 'source {0} && env'.format(path)]
-
     proc = subprocess.Popen(command, stdout=subprocess.PIPE)
-
     for line in proc.stdout:
         (key, _, value) = line.partition("=")
         os.environ[key] = value.strip()
 
+    print str_info("build"),
+
     qp_create_ninja = os.path.join(QP_ROOT, "scripts", "compilation",
                                    "qp_create_ninja.py")
 
@@ -474,7 +482,6 @@ def create_ninja_and_rc(l_installed):
 
 
 def recommendation():
-    print "Last Step:"
     path = join(QP_ROOT, "quantum_package.rc")
     print "Now :"
     print "   source {0}".format(path)

ocaml/Makefile

@@ -18,7 +18,7 @@ MLIFILES=$(wildcard *.mli)
 ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))
 ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qp_edit.native
 
-.PHONY: executables default
+.PHONY: executables default remake_executables
 
 
 default: $(ALL_TESTS) $(ALL_EXE) .gitignore
@@ -34,7 +34,7 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
 
 executables: $(QP_ROOT)/data/executables
 
-$(QP_ROOT)/data/executables:
+$(QP_ROOT)/data/executables: remake_executables
 	$(QP_ROOT)/scripts/module/create_executables_list.sh
 
 external_libs:

plugins/Casino/.gitignore

@@ -0,0 +1,23 @@
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+IRPF90_temp
+IRPF90_man
+irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
+.ninja_log
+.ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec
+save_for_casino

plugins/Casino/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Determinants

plugins/Casino/README.rst

@@ -0,0 +1,27 @@
+======
+Casino
+======
+
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. by the `update_README.py` script.
+
+`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Casino/save_for_casino.irp.f#L266>`_
+  Undocumented
+
+
+`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Casino/save_for_casino.irp.f#L1>`_
+  Undocumented
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. by the `update_README.py` script.
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+

plugins/Full_CI/.gitignore

@@ -1,4 +1,4 @@
-# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py 
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
 IRPF90_temp
 IRPF90_man
 irpf90_entities
@@ -27,6 +27,6 @@ Nuclei
 Hartree_Fock
 Properties
 target_pt2
-full_ci_no_skip
-var_pt2_ratio
 full_ci
+var_pt2_ratio
+full_ci_no_skip

plugins/Perturbation/README.rst

@@ -85,92 +85,92 @@ Documentation
   Undocumented
 
 
-`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
+`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
+`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L896>`_
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_
+`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L581>`_
+`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L581>`_
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
+`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L896>`_
+`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
+`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
   Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
+`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L845>`_
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_
+`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L530>`_
+`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_
+`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L530>`_
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
+`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
+`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
+`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L845>`_
+`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 

scripts/module/qp_install_module.py

@@ -23,10 +23,10 @@ try:
     from module_handler import get_l_module_descendant
     from update_README import Doc_key, Needed_key
     from qp_path import QP_SRC, QP_PLUGINS
-
 except ImportError:
-    print "source .quantum_package.rc"
+    print "Please check if you have source the .quantum_package.rc"
-    raise
+    print "(`source .quantum_package.rc`)"
+    print sys.exit(1)
 
 
 def save_new_module(path, l_child):
@@ -79,7 +79,7 @@ if __name__ == '__main__':
 
         l_children = arguments["<children_module>"]
 
-        path = os.path.join(QP_SRC, arguments["<name>"])
+        path = os.path.join(QP_PLUGINS, arguments["<name>"][0])
 
         print "You will create the module:"
         print path
@@ -103,6 +103,7 @@ if __name__ == '__main__':
         print l_child_reduce
         save_new_module(path, l_child_reduce)
 
+        print "This was a plugin, you can install it now"
     elif arguments["download"]:
         pass
 #        d_local = get_dict_child([QP_SRC])

src/Determinants/README.rst

@@ -605,10 +605,6 @@ Documentation
   Undocumented
 
 
-`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_casino.irp.f#L266>`_
-  Undocumented
-
-
 `psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L273>`_
   Contribution of determinants to the state-averaged density
 
@@ -815,10 +811,6 @@ Documentation
   z component of the Spin
 
 
-`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_casino.irp.f#L1>`_
-  Undocumented
-
-
 `save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_natorb.irp.f#L1>`_
   Undocumented
 

src/Ezfio_files/README.rst

@@ -38,8 +38,8 @@ Documentation
   Output file for Bitmask
 
 
-`output_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
+`output_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
-  Output file for CAS_SD
+  Output file for Casino
 
 
 `output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
@@ -62,63 +62,51 @@ Documentation
   Output file for Full_CI
 
 
-`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
+`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
-  Output file for Generators_CAS
-
-
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
   Output file for Generators_full
 
 
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
+`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
   Output file for Hartree_Fock
 
 
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
+`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
   Output file for Integrals_Bielec
 
 
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
+`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
   Output file for Integrals_Monoelec
 
 
-`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
+`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
   Output file for MO_Basis
 
 
-`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
+`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
   Output file for MOGuess
 
 
-`output_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
-  Output file for MRCC
-
-
-`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
   Output file for Nuclei
 
 
-`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
+`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
   Output file for Perturbation
 
 
-`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
+`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
   Output file for Properties
 
 
-`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
+`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
   Output file for Pseudo
 
 
-`output_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
+`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
-  Output file for QmcChem
-
-
-`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
   Output file for Selectors_full
 
 
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
+`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
   Output file for Utils