Removed org-mode

DevInstructions.org

@@ -1,20 +0,0 @@
-#+TITLE: Developper's instructions
-
-* General
-
-The developper writes org-mode files, and the OCaml files are produced
-by running the ~make~ command. Then, the OCaml files are compiled
-using ~dune~.
-
-In each directory, the =README.org= file is the entry point. It
-contains the script to generate the dune files, which should be
-created by executing ~Ctrl-C Ctrl-C~ in the appropriate code block.
-
-If necessary, some pure OCaml files can be added in the =lib=
-directory.
-
-* Basis
-
-- =Basis_poly= is a polymorphic basis
-- =Basis_gaussian= contains the basis and integrals
-- =Gaussian.Basis= is the actual Gaussian basis

Makefile

@@ -4,27 +4,25 @@
 MAKEFLAGS += --no-builtin-rules
 .SUFFIXES: 
 
-DIRS=$(shell ls */README.org | sed "s|/README.org||g")
+.PHONY: default build install uninstall test clean
-DOCS=$(patsubst %, docs/%.html, $(DIRS)) docs/index.html
 
-.PHONY: default build install uninstall test clean doc 
+default: build 
 
-default: doc build 
 
-docs/%.html: %/*.org %/lib/*.ml %/lib/*.mli %/test/*.ml
+build:
-	- ./bin/tangle.sh $*
+	top/install_printers.sh > top/lib/install_printers.ml
-
-docs/top.html: */*.org */lib/*.ml */lib/*.mli 
-	- ./bin/tangle.sh top
-
-doc: $(DOCS)
-
-build: doc
 	dune build
 
+build-prof:
+	top/install_printers.sh > top/lib/install_printers.ml
+	dune build --workspace=dune-workspace.profile
+
 test:
 	dune runtest -f
 
+test-prof:
+	dune runtest -f --workspace=dune-workspace.profile
+
 install:
 	dune install
 

README.md

@@ -33,7 +33,7 @@ How to build the project
 Run `make` to compile the libraries and executables that are
 meant to be installed.
 ```
-$ make -j
+$ make
 ```
 
 How to run tests
@@ -83,3 +83,11 @@ For more information on `opam pin`, please consult the opam documentation.
 The advantage of the opam-based method is that other opam packages can
 depend on this one, and opam will recompile them automatically as
 necessary.
+
+
+Profiling
+---------
+
+The Landmarks memory profiler can be used.
+
+

ao/README.org

@@ -1,94 +0,0 @@
-#+TITLE: Atomic Orbitals
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"Atomic basis set"
-#+end_src
-
-#+RESULTS: synopsis
-: Atomic basis set
-
-This modules contains the data structures used to characterize the
-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
-  trexio
-  qcaml.{name}
- )
-)
-""")
-   #+end_src
-
-** Dependencies
-
-   #+name: dependencies
-   #+begin_src elisp
-(libraries
- qcaml.common
- qcaml.particles
- qcaml.gaussian
- qcaml.gaussian_integrals
- qcaml.operators
- )
- (instrumentation (backend landmarks))
-   #+end_src
-
-** Modules without implementation
-
-   #+name: noimplementation
-   #+begin_src elisp
-  (modules_without_implementation ao_dim)
-   #+end_src
-
-** Extra C files
-
-   #+begin_src elisp
-   #+end_src
-
-** Parser files
-
-   #+name: lex-yacc
-   #+begin_src elisp
-   #+end_src
-
-
-
-

ao/lib/dune

@@ -1,10 +1,7 @@
-
 (library
  (name ao)
  (public_name qcaml.ao)
- (synopsis 
+ (synopsis "Atomic basis set")
-"Atomic basis set"
-  )
  (libraries
   qcaml.common
   qcaml.particles

ao/test/dune

@@ -1,4 +1,3 @@
-
 (library
  (name test_ao)
  (synopsis "Test for ao library")

common/README.org

@@ -1,95 +0,0 @@
-#+TITLE: Common
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"Utility functions used by all the other directories"
-#+end_src
-
-#+RESULTS: synopsis
-: Utility functions used by all the other directories
-
-
-* 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
-  unix
-  qcaml.{name}
- )
-)
-""")
-   #+end_src
-
-** Dependencies
-   #+name: dependencies
-   #+begin_src elisp
-(libraries
- str
- zarith
- getopt
- unix
- )
- (instrumentation (backend landmarks))
-   #+end_src
-
-** Modules without implementation
-
-   #+name: noimplementation
-   #+begin_src elisp
-   #+end_src
-
-** Extra C files
-
-   The ~util.c~ file contains small C snippets to add missing
-   functionalities to OCaml, such as support for the ~popcnt~ instruction.
-
-   #+name: c-files
-   #+begin_src elisp
- (c_names
-    util
- )
- (c_flags (:standard)
-   -Ofast -march=native -fPIC
- )
-   #+end_src
-
-** Parser
-
-   #+name: lex-yacc
-   #+begin_src elisp
-   #+end_src

common/lib/util.ml

@@ -11,17 +11,17 @@ external gamma_float : float -> float
 external popcnt : int64 -> int32 = "popcnt_bytecode" "popcnt"
 [@@unboxed] [@@noalloc]
 
-let popcnt i = (popcnt [@inlined] ) i |> Int32.to_int
+let[@inline] popcnt i = Int32.to_int (popcnt i)
 
 external trailz : int64 -> int32 = "trailz_bytecode" "trailz" "int"
 [@@unboxed] [@@noalloc]
 
-let trailz i = trailz i |> Int32.to_int
+let[@inline] trailz i = Int32.to_int (trailz i)
 
 external leadz : int64 -> int32 = "leadz_bytecode" "leadz" "int"
 [@@unboxed] [@@noalloc]
 
-let leadz i = leadz i |> Int32.to_int
+let[@inline] leadz i = Int32.to_int (leadz i)
 
 
 

dune-project

@@ -8,7 +8,7 @@
 (homepage "https://gitlab.com/scemama/qcaml")
 (documentation "https://gitlab.com/scemama/qcaml")
 
-(license "LGPL-2.1+ with OCaml linking exception")
+(license "LGPL-2.1-or-later")
 
 (maintainers
   "Anthony Scemama <scemama@irsamc.ups-tlse.fr>"
@@ -34,7 +34,7 @@ in quantum chemistry.")
     zarith
     alcotest
     domainslib
-    (landmarks-ppx (and :dev (>= 1.4)))
+;   (landmarks-ppx (and :dev (>= 1.4))) 
   )
 )
 

dune-workspace.profile

@@ -0,0 +1,14 @@
+(lang dune 2.9)
+
+(context default)
+
+(context
+  (default
+    (name profiling)
+    (instrument_with landmarks)
+    (env
+      (_ (env-vars ("OCAML_LANDMARKS" "auto")))
+    )
+  )
+)
+

gaussian/README.org

@@ -1,88 +0,0 @@
-#+TITLE: Gaussian
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"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
- (instrumentation (backend landmarks))
-
-   #+name: dependencies
-   #+begin_src elisp
-(libraries
- qcaml.common
- qcaml.particles
- )
- (instrumentation (backend landmarks))
-   #+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_integrals/README.org

@@ -1,93 +0,0 @@
-#+TITLE: Gaussian integrals
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"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
-  unix
-  trexio
-  domainslib
-  qcaml.{name}
- )
-)
-""")
-   #+end_src
-
-** Dependencies
-
-   #+name: dependencies
-   #+begin_src elisp
-(libraries
- qcaml.common
- qcaml.linear_algebra
- qcaml.gaussian
- qcaml.operators
- )
- (instrumentation (backend landmarks))
-   #+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
-
-
-
-

linear_algebra/README.org

@@ -1,87 +0,0 @@
-#+TITLE: Linear Algebra
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"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
- )
- (instrumentation (backend landmarks))
-   #+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/README.org

@@ -1,86 +0,0 @@
-#+TITLE: Molecular orbitals
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"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
- )
- (instrumentation (backend landmarks))
-   #+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/README.org

@@ -1,86 +0,0 @@
-#+TITLE: Operators
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"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
- )
- (instrumentation (backend landmarks))
-   #+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
-
-
-
-

particles/README.org

@@ -1,99 +0,0 @@
-#+TITLE: Common
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"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
-  trexio
-  qcaml.{name}
- )
-)
-""")
-   #+end_src
-
-** Dependencies
-
-   #+name: dependencies
-   #+begin_src elisp
-(libraries
- trexio
- qcaml.common
- )
- (instrumentation (backend landmarks))
-   #+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
-
-
-
-

perturbation/README.org

@@ -1,87 +0,0 @@
-#+TITLE: Perturbation
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"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
- )
- (instrumentation (backend landmarks))
-   #+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.opam

@@ -6,7 +6,7 @@ QCaml provides a programming framewrok work wave function methods
 in quantum chemistry."""
 maintainer: ["Anthony Scemama <scemama@irsamc.ups-tlse.fr>"]
 authors: ["Anthony Scemama <scemama@irsamc.ups-tlse.fr>"]
-license: "LGPL-2.1+ with OCaml linking exception"
+license: "LGPL-2.1-or-later"
 homepage: "https://gitlab.com/scemama/qcaml"
 doc: "https://gitlab.com/scemama/qcaml"
 bug-reports: "https://gitlab.com/scemama/qcaml/issues"
@@ -20,7 +20,6 @@ depends: [
   "zarith"
   "alcotest"
   "domainslib"
-  "landmarks-ppx" {dev & >= "1.4"}
   "odoc" {with-doc}
 ]
 build: [

qcaml/README.org

@@ -1,92 +0,0 @@
-#+TITLE: QCaml
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"Main QCaml entry point"
-#+end_src
-
-#+RESULTS: synopsis
-: Main QCaml entry point
-
-
-* File generation                                                  :noexport:
-
-   Use [C-c C-c] on the code below. This will create the dune files
-   and the =qcaml.ml= file.
-
-   #+header: :noweb yes
-   #+header: :var name=(file-name-directory buffer-file-name)
-   #+header: :var dune="lib/dune"
-   #+header: :var mlfile="lib/qcaml.ml"
-   #+header: :var dunetest="test/dune"
-   #+header: :var dependencies=dependencies
-   #+begin_src python :exports none :results output none
-name = name.split('/')[-2]
-synopsis = """
-<<synopsis>>
-"""
-
-excluded_modules = [ "top" ]
-
-dependencies = '\n '.join([x[0] for x in dependencies if x[0].replace("qcaml.","") not in excluded_modules])
-
-with open(dune,'w') as f:
-    f.write(f"""
-(library
- (name qcaml)
- (public_name qcaml)
- (synopsis {synopsis}  )
- (libraries
- {dependencies}
- )
- (instrumentation (backend landmarks))
- <<noimplementation>>
- <<c-files>>
-)
-<<lex-yacc>>
-""")
-
-with open(dunetest,'w') as f:
-    f.write(f"""
-(library
- (name test_qcaml)
- (synopsis "Test for qcaml library")
- (libraries
-  alcotest
-  qcaml
- )
-)
-""")
-
-with open(mlfile,'w') as f:
-    s = dependencies.split()
-    s = [x.replace("qcaml.","") for x in s ]
-    s = [x.capitalize() for x in s]
-    s = [ f"module {x} = {x}\n" for x in s ]
-    s = ''.join(s)
-    f.write("(* Auto-generated by qcaml/README.org *)\n")
-    f.write(s)
-
-   #+end_src
-
-
-   #+name: dependencies
-   #+begin_src sh :output value
-grep "public_name" ../*/lib/dune | grep -v "qcaml)" | cut -d ' ' -f 3 | tr ')' ' '
-   #+end_src
-
-   #+RESULTS: dependencies
-   | qcaml.ao                 |
-   | qcaml.common             |
-   | qcaml.gaussian           |
-   | qcaml.gaussian_integrals |
-   | qcaml.linear_algebra     |
-   | qcaml.mo                 |
-   | qcaml.operators          |
-   | qcaml.particles          |
-   | qcaml.perturbation       |
-   | qcaml.simulation         |
-   | qcaml.top                |

simulation/README.org

@@ -1,91 +0,0 @@
-#+TITLE: Simulation
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"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
- )
- (instrumentation (backend landmarks))
-   #+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
-
-
-
-

top/README.org

@@ -1,43 +0,0 @@
-#+TITLE: Top-level
-#+SETUPFILE: ../docs/theme.setup
-
-* Summary
-
-#+name: synopsis
-#+begin_src ocaml :exports none :results value
-"Installs pretty printers for top-level"
-#+end_src
-
-#+RESULTS: synopsis
-: Installs pretty printers for top-level
-
-
-* 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)
-   #+begin_src python :exports none :results output none
-name = name.split('/')[-2]
-synopsis = """
-<<synopsis>>
-"""
-
-with open("lib/dune",'w') as f:
-    f.write(f"""
-(library
- (name {name})
- (public_name qcaml.{name})
- (synopsis {synopsis}  )
- (modes byte)
- (libraries
-  compiler-libs.toplevel
-  qcaml
- )
- (instrumentation (backend landmarks))
-)
-""")
-   #+end_src

top/install_printers.org

@@ -1,73 +0,0 @@
-#+begin_src elisp tangle: no :results none :exports none
-(setq pwd (file-name-directory buffer-file-name))
-(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
-(setq lib (concat pwd "lib/"))
-(setq testdir (concat pwd "test/"))
-(setq mli (concat lib name ".mli"))
-(setq ml  (concat lib name ".ml"))
-(setq test-ml  (concat testdir name ".ml"))
-(org-babel-tangle)
-#+end_src 
-
-
-* Intall printers                                                  :noexport:
-  :PROPERTIES:
-  :header-args: :noweb yes :comments both
-  :END:
-
-  Installs printers in the top-level environment.
-
-  All printers are fetched automatically.
-  
-  #+NAME: raw_printers
-  #+begin_src sh :results output raw :exports none
-grep "val pp " ../*/lib/*.mli \
-    | cut -d ":" -f 1 \
-    | sed 's|^../||' \
-    | sed 's|.mli||' \
-    | sed 's|/lib/| |' \
-    | sed 's/[^ ]*/\u&/g' \
-    | sed 's| |.|' \
-    | grep -v Top.Install_printers
-  #+end_src
-
-
-  #+NAME: printers
-  #+begin_src python :results output raw :var p=raw_printers :exports none
-result = []
-for l in p.split():
-    dir, module = l.split('.')
-    if dir == module:
-        e = f'"{module}.pp" ;'
-    else:
-        e = f'"{dir}.{module}.pp" ;'
-    result.append(e)
-result = '\n'.join(result)
-print(result)
-  #+end_src
-
-  
-
-  #+begin_src ocaml :tangle (eval ml) :exports none
-let printers =
-  [
-    <<printers()>>
-  ]
-
-let eval_exn str =
-  let lexbuf = Lexing.from_string str in
-  let phrase = !Toploop.parse_toplevel_phrase lexbuf in
-  Toploop.execute_phrase false Format.err_formatter phrase
-
-
-let rec install_printers = function
-  | [] -> eval_exn "#require \"lacaml.top\";;"
-  | printer :: printers ->
-      let cmd = Printf.sprintf "#install_printer %s;;" printer in
-      eval_exn cmd && install_printers printers
-
-let () =
-  if not (install_printers printers) then
-    Format.eprintf "Problem installing QCaml-printers@."
-
-  #+end_src

top/lib/dune

@@ -3,11 +3,12 @@
  (name top)
  (public_name qcaml.top)
  (synopsis 
-"Installs pretty printers for top-level."
+"Installs pretty printers for top-level"
   )
  (modes byte)
  (libraries
   compiler-libs.toplevel
   qcaml
  )
+ (instrumentation (backend landmarks))
 )

top/lib/install_printers.ml

@@ -1,35 +1,5 @@
-(* [[file:~/QCaml/top/install_printers.org::*Intall printers][Intall printers:3]] *)
 let printers =
   [
-    "Ao.Basis.pp" ;
-    "Ao.Basis_gaussian.pp" ;
-    "Common.Angular_momentum.pp" ;
-    "Common.Bitstring.pp" ;
-    "Common.Charge.pp" ;
-    "Common.Coordinate.pp" ;
-    "Common.Powers.pp" ;
-    "Common.Range.pp" ;
-    "Common.Spin.pp" ;
-    "Common.Zkey.pp" ;
-    "Gaussian.Atomic_shell.pp" ;
-    "Gaussian.Atomic_shell_pair.pp" ;
-    "Gaussian.Atomic_shell_pair_couple.pp" ;
-    "Gaussian.Basis.pp" ;
-    "Gaussian.Contracted_shell.pp" ;
-    "Gaussian.General_basis.pp" ;
-    "Linear_algebra.Matrix.pp" ;
-    "Mo.Basis.pp" ;
-    "Mo.Class.pp" ;
-    "Mo.Fock.pp" ;
-    "Mo.Frozen_core.pp" ;
-    "Mo.Hartree_fock.pp" ;
-    "Mo.Localization.pp" ;
-    "Particles.Electrons.pp" ;
-    "Particles.Element.pp" ;
-    "Particles.Nuclei.pp" ;
-    "Particles.Zmatrix.pp" ;
-    "Perturbation.Mp2.pp" ;
-    "Simulation.pp" ;
 
   ]
 
@@ -48,4 +18,4 @@ let rec install_printers = function
 let () =
   if not (install_printers printers) then
     Format.eprintf "Problem installing QCaml-printers@."
-(* Intall printers:3 ends here *)
+