Merge branch 'master' of github.com:TApplencourt/quantum_package

.travis.yml

@@ -12,7 +12,7 @@ before_script:
 script: 
   - ./setup_environment.py
   - source ./quantum_package.rc
-  - qp_create_ninja.py --production ./config/gfortran_example.cfg
+  - qp_create_ninja.py --production ./config/gfortran.cfg
   - ninja
   - cd ocaml ; make ; cd -
   - cd testing_no_regression ; ./unit_test.py

COMPILE_RUN.md

@@ -1,31 +1,41 @@
 # Compile
 
-We need to create the file who contain all the tree dependencies for the binaries. It's not a MakeFile, but a Ninja file. (So don't type `make` is hopeless, type `ninja` instead)
+We need to create the file which contains all the tree dependencies for the
+binaries.  It's not a Makefile, but a Ninja file (so don't type `make` is
+hopeless, type `ninja` instead).
 
-The script to create the dependencies file (aka `build.ninja`) is `create_ninja_build.py`.
+The script to create the dependency file (aka `build.ninja`) is
+`qp_create_ninja.py`.
 
 ## What utilization of the code will you do?
 
-   * If you only want the binaries (for production workflow) use the flag `--production` in when calling this script. It's quicker 
+* If you only want the binaries (for production workflow) use the flag
+  `--production` in when calling this script. It's quicker 
+* Else if you are a developer and you want to be able to compile specific
+  modules use: `--development`
 
-   * Else if you are a developer and you want to be able to only compile one specific module use: `--development`
+## Compilation Flags
 
-## Compilation Flag
-
-You need to specify all the flag useful for the compilation:   like the optimization one, the mkl one .``$QP_ROOT/config`` contains ``ifort.cfg`` and ``gfortran.cfg`` files which have the compiler flags that will be used to compile the code. You can edit these files to modify the compiling option. Put the file path when calling `create_ninja_build.py`
+You need to specify all the flags useful for the compilation:  like the
+optimization flags, the Lapack libary, etc.  ``$QP_ROOT/config`` contains
+``ifort.cfg`` and ``gfortran.cfg`` containing the compiler flags that will be
+used.  You can edit these files to modify the compiling options. 
 
 ## Example to create the Ninja file
 
-`create_ninja_build.py --production $QP_ROOT/config/ifort.cfg`
+`qp_create_ninja.py --production $QP_ROOT/config/ifort.cfg`
 
 # WARNING
 
-For now reload this command if you add a `IRP.f90` or `EZFIO.cfg` file or modify the `NEED_CHILDREN_MODULE`!
+For now you need to execute this command if you add a `irp.f` or `EZFIO.cfg`
+file or modify the `NEED_CHILDREN_MODULE`!
 
-## Compile
+## Compiling
 
-Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja` elsewhere). The compilation will take approximately 3 min.
+Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja`
+elsewhere). The compilation will take approximately 3 min.
 
-If you have set the `--developement` flag in a specific module you can go in the corresponding IRPF90_temp and run `ninja` to only make the module and submodule binaries. (You can use the `-f` option too)
+If you have set the `--developement` flag in a specific module you can go in
+the corresponding module directory and run `ninja` to build only this module.
 
-Now go in `$QP_ROOT/ocaml` and type `make`
+Finally, go in `$QP_ROOT/ocaml` and type `make`

ocaml/.gitignore

@@ -5,7 +5,6 @@ qptypes_generator.byte
 _build
 qp_basis_clean.native
 qp_create_ezfio_from_xyz.native
-qp_edit.native
 qp_print.native
 qp_run.native
 qp_set_ddci.native
@@ -33,17 +32,16 @@ test_molecule
 test_point3d
 qp_basis_clean
 qp_create_ezfio_from_xyz
-qp_edit
 qp_print
 qp_run
 qp_set_ddci
 qp_set_mo_class
-Input_pseudo.ml
-Input_integrals_bielec.ml
-Input_hartree_fock.ml
-Input_perturbation.ml
 Input_determinants.ml
+Input_hartree_fock.ml
+Input_integrals_bielec.ml
+Input_perturbation.ml
 Input_properties.ml
+Input_pseudo.ml
 qp_edit.ml
 qp_edit
 qp_edit.native

setup_environment.py

@@ -8,6 +8,20 @@ import pprint
 
 from os.path import join
 
+def finalize():
+    path = join(QP_ROOT, "quantum_package.rc")
+    print "For more info on compiling the code, read the COMPILE_RUN.md file."
+    print ""
+    print "You can check {0} and run:".format(path)
+    print ""
+    print "   source {0}".format(path)
+    print "   qp_create_ninja.py --production $QP_ROOT/config/ifort.cfg"
+    print "   ninja"
+    print "   make -C ocaml"
+    print ""
+    sys.exit()
+
+
 #  __                           _
 # /__ |   _  |_   _. |   o ._ _|_ _
 # \_| |_ (_) |_) (_| |   | | | | (_)
@@ -16,8 +30,10 @@ from os.path import join
 QP_ROOT = os.getcwd()
 QP_ROOT_BIN = join(QP_ROOT, "bin")
 QP_ROOT_INSTALL = join(QP_ROOT, "install")
+os.environ["PATH"] = ":".join( [QP_ROOT_BIN,os.environ["PATH"] ] )
 
-d_dependancy = {
+
+d_dependency = {
     "ocaml": ["m4", "curl", "zlib", "patch", "gcc"],
     "m4": ["make"],
     "curl": ["make"],
@@ -142,7 +158,7 @@ def check_python():
         sys.exit(1)
 
 
-def check_avabiliy(binary):
+def check_availabiliy(binary):
 
     if binary == "python":
         check_python()
@@ -174,15 +190,17 @@ print """
 """
 
 # Check all the other
-for i in d_dependancy.keys():
-    print "Checking if you have {0} avalaible...".format(i),
+length = max( [ len(i) for i in d_dependency ] )
+fmt = "%"+str(length)+"s"
+for i in d_dependency.keys():
+    print "Checking if %s is avalaible..."%( i.center(length) ),
 
-    r = check_avabiliy(i)
+    r = check_availabiliy(i)
     if r:
-        print "OK"
+        print "[ OK ]"
         l_installed[i] = r.strip()
     else:
-        print "We will try to compile if from source in a few moment"
+        print "Will compile it"
         l_need.append(i)
 
 # Expend the need_stuff for all the genealogy
@@ -191,7 +209,7 @@ d_need_genealogy = dict()
 
 for need in l_need:
     d_need_genealogy[need] = None
-    for childen in d_dependancy[need]:
+    for childen in d_dependency[need]:
         if childen not in l_installed:
             d_need_genealogy[childen] = None
 
@@ -220,11 +238,11 @@ print """
 """
 
 if l_need_genealogy:
-    print "You need to install"
+    print "You need to install:"
     pprint.pprint(l_need_genealogy)
 else:
-    print "Nothing to do"
-    sys.exit()
+    print "Nothing to do."
+    finalize()
 
 if "ninja" in l_need_genealogy:
 
@@ -286,7 +304,7 @@ for need in l_need_genealogy:
                 "   descr = {0}".format(descr), ""]
 
     # Build to install
-    l_dependancy = [d_info[i].default_path for i in d_dependancy[need] if i in l_need_genealogy]
+    l_dependancy = [d_info[i].default_path for i in d_dependency[need] if i in l_need_genealogy]
 
     l_build += ["build {0}: install {1} {2}".format(d_info[need].default_path,
                                                     archive_path,
@@ -301,7 +319,7 @@ with open(path, "w+") as f:
     f.write("\n".join(l_string))
 
 print "Done"
-print "You can check at {0}".format(path)
+print "You can check {0}".format(path)
 
 print """
 # ~#~#~#~#~#~#~#~#~ #
@@ -310,7 +328,7 @@ print """
 """
 
 if [i for i in l_need_genealogy if i not in "ocaml"]:
-    subprocess.check_call("./bin/ninja -C install", shell=True)
+    subprocess.check_call("ninja -C install", shell=True)
 
 print "Done"
 
@@ -327,7 +345,7 @@ if "ocaml" in l_need_genealogy:
 
     l_cmd = ["cd install &&",
              "wget {0} -O {1} -o /dev/null &&".format(url, path_archive),
-             "./scripts/install_ocaml.sh --fast"]
+             "./scripts/install_ocaml.sh"]
 
     os.system(" ".join(l_cmd))
 
@@ -378,6 +396,5 @@ path = join(QP_ROOT, "quantum_package.rc")
 with open(path, "w+") as f:
     f.write("\n".join(l_rc))
 
-print "Done"
-print "You can check at {0}".format(path)
-print "Don't forget to source it"
+print "Done."
+finalize()

testing_no_regression/unit_test.py

@@ -163,6 +163,7 @@ def run_hf(geo, basis, mult=1, pseudo=False, remove_after_sucess=True):
 
     ref_energy["sto-3g"]["methane"] = Energy(-39.7267433402, None)
     ref_energy["vdz"]["SO2"] = Energy(None, -41.48912297776174)
+#   ref_energy["vdz"]["HBO"] = Energy(None, -19.1198231418)
     ref_energy["vdz"]["HBO"] = Energy(None, -19.1198254041)
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #