Cleaned readme for auto-generation

ao/README.org

@@ -0,0 +1,87 @@
+#+TITLE: Atomic Orbitals
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Atomic basis set"
+#+end_src
+
+#+RESULTS: synopsis
+: Atomic basis set
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.common
+ qcaml.particles
+ qcaml.gaussian
+ qcaml.gaussian_integrals
+ qcaml.operators
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

ao/lib/dune

@@ -1,8 +1,10 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name ao)
  (public_name qcaml.ao)
+ (synopsis 
+"Atomic basis set"
+  )
  (libraries
   qcaml.common
   qcaml.particles
@@ -10,4 +12,7 @@
   qcaml.gaussian_integrals
   qcaml.operators
   )
- (synopsis "Atomic basis set."))
+ 
+ 
+)
+

ao/test/dune

@@ -1,10 +1,9 @@
+
 (library
- (name test_ao_basis)
+ (name test_ao)
+ (synopsis "Test for ao library")
  (libraries
   alcotest
-  qcaml.common
-  qcaml.linear_algebra
-  qcaml.gaussian_integrals
   qcaml.ao
  )
- (synopsis "Tests for the AO basis"))
+)

common/README.org

@@ -2,60 +2,80 @@
 #+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
 
 
-This directory contains many utility functions used by all the other directories.
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Utility functions used by all the other directories."
+#+end_src
+
+#+RESULTS: synopsis
+: Utility functions used by all the other directories.
+
 
 * Dune files                                                         :noexport:
-  :PROPERTIES:
-  :dune:       lib/dune
-  :dune-test:  test/dune
-  :header-args: :noweb yes 
-  :END:
 
-** Headers
+** Generate dune files
-   #+begin_src elisp :tangle (org-entry-get nil "dune" t)
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
 (library
-   #+end_src
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
 
-   #+begin_src elisp :tangle (org-entry-get nil "dune-test" t)
+with open(dunetest,'w') as f:
+    f.write(f"""
 (library
-   #+end_src
+ (name test_{name})
-
+ (synopsis "Test for {name} library")
-** Library
-   
-*** General information
-     #+begin_src elisp :tangle (org-entry-get nil "dune" t)
- (name common)
- (public_name qcaml.common)
- (synopsis "General utilities used in all QCaml libraries.")
-     #+end_src
-
-     #+begin_src elisp :tangle (org-entry-get nil "dune-test" t)
- (name test_common)
- (synopsis "Test for common library")
-     #+end_src
-
-*** Dependencies
-     #+begin_src elisp :tangle (org-entry-get nil "dune" t)
  (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
  str
  zarith
  getopt
  )
    #+end_src
 
-     #+begin_src elisp :tangle (org-entry-get nil "dune-test" t)
+** Modules without implementation
- (libraries
+    
-  alcotest
+   #+name: noimplementation
-  qcaml.common
+   #+begin_src elisp
- )
    #+end_src
 
-*** Extra C files
+** Extra C files
 
    The ~util.c~ file contains small C snippets to add missing
    functionalities to OCaml, such as support for the ~popcnt~ instruction.
 
-     #+begin_src elisp :tangle (org-entry-get nil "dune" t)
+   #+name: c-files
+   #+begin_src elisp 
  (c_names
     util
  )
@@ -64,14 +84,8 @@ This directory contains many utility functions used by all the other directories
  )
    #+end_src
 
-** Footers
+** Parser
 
-   #+begin_src elisp :tangle (org-entry-get nil "dune" t)
+   #+name: lex-yacc
-)
+   #+begin_src elisp 
    #+end_src
-
-   #+begin_src elisp :tangle (org-entry-get nil "dune-test" t)
-)
-   #+end_src
-
-   

common/lib/dune

@@ -1,9 +1,10 @@
-(library
 
+(library
  (name common)
  (public_name qcaml.common)
- (synopsis "General utilities used in all QCaml libraries.")
+ (synopsis 
-
+"Utility functions used by all the other directories."
+  )
  (libraries
   str
   zarith
@@ -16,5 +17,5 @@
   (c_flags (:standard)
     -Ofast -march=native -fPIC
   )
-
 )
+

common/test/dune

@@ -1,11 +1,9 @@
-(library
 
+(library
  (name test_common)
  (synopsis "Test for common library")
-
  (libraries
   alcotest
   qcaml.common
  )
-
 )

gaussian/README.org

@@ -0,0 +1,84 @@
+#+TITLE: Gaussian
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Gaussian basis sets"
+#+end_src
+
+#+RESULTS: synopsis
+: Gaussian basis sets
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.common
+ qcaml.particles
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

gaussian/lib/dune

@@ -1,11 +1,15 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name gaussian)
  (public_name qcaml.gaussian)
+ (synopsis 
+"Gaussian basis sets"
+  )
  (libraries
-        str
   qcaml.common
   qcaml.particles
   )
- (synopsis "Gaussian basis sets."))
+ 
+ 
+)
+

gaussian/test/dune

@@ -1,8 +1,9 @@
+
 (library
- (name test_gaussian_basis)
+ (name test_gaussian)
+ (synopsis "Test for gaussian library")
  (libraries
   alcotest
-  qcaml.particles
   qcaml.gaussian
  )
- (synopsis "Tests for Gaussian basis sets"))
+)

gaussian_integrals/README.org

@@ -0,0 +1,87 @@
+#+TITLE: Gaussian integrals
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Integrals on the Gaussian basis sets"
+#+end_src
+
+#+RESULTS: synopsis
+: Integrals on the Gaussian basis sets
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.common
+ qcaml.linear_algebra
+ qcaml.gaussian
+ qcaml.operators
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+(modules_without_implementation matrix_on_basis)
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

gaussian_integrals/lib/dune

@@ -1,14 +1,17 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name gaussian_integrals)
  (public_name qcaml.gaussian_integrals)
+ (synopsis 
+"Integrals on the Gaussian basis sets"
+  )
  (libraries
-        str
   qcaml.common
   qcaml.linear_algebra
   qcaml.gaussian
   qcaml.operators
   )
  (modules_without_implementation matrix_on_basis)
- (synopsis "Integrals on the Gaussian basis sets."))
+ 
+)
+

gaussian_integrals/test/dune

@@ -1,8 +1,9 @@
+
 (library
  (name test_gaussian_integrals)
+ (synopsis "Test for gaussian_integrals library")
  (libraries
   alcotest
-  qcaml.particles
   qcaml.gaussian_integrals
  )
- (synopsis "Tests for integrals on the Gaussian basis sets"))
+)

linear_algebra/README.org

@@ -0,0 +1,84 @@
+#+TITLE: Linear Algebra
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Linear algebra utilities of QCaml libraries."
+#+end_src
+
+#+RESULTS: synopsis
+: Linear algebra utilities of QCaml libraries.
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.common
+ lacaml
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

linear_algebra/lib/dune

@@ -1,10 +1,15 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name linear_algebra)
  (public_name qcaml.linear_algebra)
+ (synopsis 
+"Linear algebra utilities of QCaml libraries."
+  )
  (libraries
   qcaml.common
   lacaml
   )
- (synopsis "Linear algebra utilities of QCaml libraries."))
+ 
+ 
+)
+

linear_algebra/test/dune

@@ -1,7 +1,9 @@
+
 (library
  (name test_linear_algebra)
+ (synopsis "Test for linear_algebra library")
  (libraries
   alcotest
   qcaml.linear_algebra
  )
- (synopsis "Tests for linear algebra"))
+)

mo/README.org

@@ -0,0 +1,83 @@
+#+TITLE: Molecular orbitals
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Molecular orbitals"
+#+end_src
+
+#+RESULTS: synopsis
+: Parameteried operators, such as F12 and range-separation
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.simulation
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

mo/lib/dune

@@ -1,9 +1,14 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name mo)
  (public_name qcaml.mo)
+ (synopsis 
+"Molecular orbitals"
+  )
  (libraries
   qcaml.simulation
   )
- (synopsis "Molecular orbitals."))
+ 
+ 
+)
+

mo/test/dune

@@ -1,12 +1,9 @@
+
 (library
- (name test_mo_basis)
+ (name test_mo)
+ (synopsis "Test for mo library")
  (libraries
   alcotest
   qcaml.mo
  )
- (synopsis "Tests for the MO basis"))
+)
-
-
-
-
-

operators/README.org

@@ -0,0 +1,83 @@
+#+TITLE: Operators
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Parameteried operators, such as F12 and range-separation"
+#+end_src
+
+#+RESULTS: synopsis
+: Parameteried operators, such as F12 and range-separation
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.common
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

operators/lib/dune

@@ -1,10 +1,14 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name operators)
  (public_name qcaml.operators)
+ (synopsis 
+"Parameteried operators, such as F12 and range-separation"
+  )
  (libraries
-        str
   qcaml.common
   )
- (synopsis "Parameterized operators"))
+ 
+ 
+)
+

operators/test/dune

@@ -0,0 +1,9 @@
+
+(library
+ (name test_operators)
+ (synopsis "Test for operators library")
+ (libraries
+  alcotest
+  qcaml.operators
+ )
+)

particles/README.org

@@ -0,0 +1,94 @@
+#+TITLE: Common
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Information relative to particles (electrons and nuclei)."
+#+end_src
+
+#+RESULTS: synopsis
+: Information relative to particles (electrons and nuclei).
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.common
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+(modules_without_implementation
+ xyz_ast
+ )
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+(ocamllex
+ (modules
+  nuclei_lexer
+  ))
+(ocamlyacc
+ (modules
+  xyz_parser
+  ))
+   #+end_src
+
+
+
+   

particles/lib/dune

@@ -1,17 +1,23 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name particles)
  (public_name qcaml.particles)
+ (synopsis 
+"Information relative to particles (electrons and nuclei)."
+  )
  (libraries
-        str
   qcaml.common
   )
- (modules_without_implementation xyz_ast)
+ (modules_without_implementation
- (synopsis "Defines nuclei and electrons."))
+  xyz_ast
+  )
+ 
+)
 (ocamllex
-  (modules nuclei_lexer)
+ (modules
-)
+  nuclei_lexer
+  ))
 (ocamlyacc
-  (modules xyz_parser)
+ (modules
-)
+  xyz_parser
+  ))

particles/test/dune

@@ -1,7 +1,9 @@
+
 (library
  (name test_particles)
+ (synopsis "Test for particles library")
  (libraries
   alcotest
   qcaml.particles
  )
- (synopsis "Tests for particles"))
+)

perturbation/README.org

@@ -0,0 +1,84 @@
+#+TITLE: Perturbation
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Perturbation theory"
+#+end_src
+
+#+RESULTS: synopsis
+: Perturbation theory
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.simulation
+ qcaml.mo
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

perturbation/lib/dune

@@ -1,10 +1,15 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name perturbation)
  (public_name qcaml.perturbation)
+ (synopsis 
+"Perturbation theory"
+  )
  (libraries
   qcaml.simulation
   qcaml.mo
   )
- (synopsis "Perturbation theory."))
+ 
+ 
+)
+

perturbation/test/dune

@@ -1,13 +1,9 @@
+
 (library
  (name test_perturbation)
+ (synopsis "Test for perturbation library")
  (libraries
   alcotest
-  qcaml.mo
   qcaml.perturbation
  )
- (synopsis "Tests for the perturbation"))
+)
-
-
-
-
-

qcaml/README.org

@@ -0,0 +1,91 @@
+#+TITLE: QCaml
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Main QCaml entry point"
+#+end_src
+
+#+RESULTS: synopsis
+: Main QCaml entry point
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.ao
+ qcaml.common
+ qcaml.gaussian
+ qcaml.gaussian_integrals
+ qcaml.mo
+ qcaml.operators
+ qcaml.particles
+ qcaml.perturbation
+ qcaml.simulation
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

qcaml/lib/dune

@@ -1,8 +1,10 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name qcaml)
- (public_name qcaml)
+ (public_name qcaml.qcaml)
+ (synopsis 
+"Main QCaml entry point"
+  )
  (libraries
   qcaml.ao
   qcaml.common
@@ -14,4 +16,7 @@
   qcaml.perturbation
   qcaml.simulation
   )
- (synopsis "Main QCaml entry point"))
+ 
+ 
+)
+

qcaml/test/dune

@@ -0,0 +1,9 @@
+
+(library
+ (name test_qcaml)
+ (synopsis "Test for qcaml library")
+ (libraries
+  alcotest
+  qcaml.qcaml
+ )
+)

simulation/README.org

@@ -0,0 +1,88 @@
+#+TITLE: Simulation
+#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
+
+#+name: synopsis
+#+begin_src ocaml :export output raw
+"Data describing a simulation (AOs, operators, nuclear coordinate,...)"
+#+end_src
+
+#+RESULTS: synopsis
+: Data describing a simulation (AOs, operators, nuclear coordinate,...)
+
+
+* Dune files                                                         :noexport:
+  
+** Generate dune files
+
+   Use [C-c C-c] on the code below to create the output for the dune files
+
+   #+header: :noweb strip-export
+   #+header: :var name=(file-name-directory buffer-file-name) 
+   #+header: :var dune="lib/dune"
+   #+header: :var dunetest="test/dune"
+   #+begin_src python :exports none :results output none
+name = name.split('/')[-2]
+synopsis = """
+<<synopsis>>
+"""
+
+with open(dune,'w') as f:
+    f.write(f"""
+(library
+ (name {name})
+ (public_name qcaml.{name})
+ (synopsis {synopsis}  )
+ <<dependencies>>
+ <<noimplementation>>
+ <<c-files>>
+)
+<<lex-yacc>>
+""")
+
+with open(dunetest,'w') as f:
+    f.write(f"""
+(library
+ (name test_{name})
+ (synopsis "Test for {name} library")
+ (libraries
+  alcotest
+  qcaml.{name}
+ )
+)
+""")
+   #+end_src
+
+** Dependencies
+
+   #+name: dependencies
+   #+begin_src elisp 
+(libraries
+ qcaml.common
+ qcaml.particles
+ qcaml.gaussian
+ qcaml.gaussian_integrals
+ qcaml.operators
+ qcaml.ao
+ )
+   #+end_src
+
+** Modules without implementation
+    
+   #+name: noimplementation
+   #+begin_src elisp
+   #+end_src
+
+** Extra C files
+
+   #+begin_src elisp
+   #+end_src
+
+** Parser files
+
+   #+name: lex-yacc
+   #+begin_src elisp
+   #+end_src
+
+
+
+   

simulation/lib/dune

@@ -1,8 +1,10 @@
-; name = name of the supermodule that will wrap all source files as submodules
+
-; public_name = name of the library for ocamlfind and opam
 (library
  (name simulation)
  (public_name qcaml.simulation)
+ (synopsis 
+"Data describing a simulation (AOs, operators, nuclear coordinate,...)"
+  )
  (libraries
   qcaml.common
   qcaml.particles
@@ -11,4 +13,7 @@
   qcaml.operators
   qcaml.ao
   )
- (synopsis "Contains data describing a simulation (AOs, operators, nuclear coordinate,...)"))
+ 
+ 
+)
+

simulation/test/dune

@@ -0,0 +1,9 @@
+
+(library
+ (name test_simulation)
+ (synopsis "Test for simulation library")
+ (libraries
+  alcotest
+  qcaml.simulation
+ )
+)

test/dune

@@ -5,10 +5,10 @@
   test_common
   test_linear_algebra
   test_particles
-  test_gaussian_basis
+  test_gaussian
   test_gaussian_integrals
-  test_ao_basis
+  test_ao
-  test_mo_basis
+  test_mo
   test_perturbation
 ))
 

test/run_tests.ml

@@ -8,11 +8,11 @@ let test_suites: unit Alcotest.test list = [
   "Linear_algebra.Vector", Test_linear_algebra.Vector.tests;
   "Particles.Nuclei", Test_particles.Nuclei.tests;
   "Particles.Electrons", Test_particles.Electrons.tests;
-  "Gaussian_basis.General_basis", Test_gaussian_basis.General_basis.tests;
+  "Gaussian_basis.General_basis", Test_gaussian.General_basis.tests;
-  "Ao_basis.Ao_basis_gaussian", Test_ao_basis.Ao_basis_gaussian.tests;
+  "Ao_basis.Ao_basis_gaussian", Test_ao.Ao_basis_gaussian.tests;
-  "Ao_basis.Ao_basis", Test_ao_basis.Ao_basis.tests;
+  "Ao_basis.Ao_basis", Test_ao.Ao_basis.tests;
-  "Mo.Guess", Test_mo_basis.Guess.tests;
+  "Mo.Guess", Test_mo.Guess.tests;
-  "Mo.Hartree_Fock", Test_mo_basis.Hf.tests;
+  "Mo.Hartree_Fock", Test_mo.Hf.tests;
   "Perturbation.Mp2", Test_perturbation.Mp2.tests;
 ]