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

README.md

@@ -1,7 +1,9 @@
 ## IMPORTANT
 
-If you have problems upgrading to the current version, consider re-installing everything from scratch including the OCaml compiler.
+If you have problems upgrading to the current version, first try
-To do this, you will have to remove the `quantum_package` directory **and** the `$HOME/.opam` directory as well.
+`qp_upgrade_ocaml.sh`. If it fails, then consider re-installing everything from
+scratch including the OCaml compiler.  To do this, you will have to remove the
+`quantum_package` directory **and** the `$HOME/.opam` directory as well.
 
 
 

configure

@@ -49,7 +49,7 @@ QP_ROOT_INSTALL = join(QP_ROOT, "install")
 os.environ["PATH"] = os.environ["PATH"] + ":" + QP_ROOT_BIN
 
 d_dependency = {
-    "ocaml": ["m4", "curl", "zlib", "patch", "gcc", "zeromq"],
+    "ocaml": ["m4", "curl", "zlib", "patch", "gcc", "zeromq", "gmp"],
     "m4": ["make"],
     "curl": ["make"],
     "zlib": ["gcc", "make"],
@@ -67,7 +67,8 @@ d_dependency = {
     "ninja": ["g++", "python"],
     "make": [],
     "p_graphviz": ["python"],
-    "bats": []
+    "bats": [],
+    "gmp" : ["make", "g++"]
 }
 
 from collections import namedtuple
@@ -136,6 +137,11 @@ zeromq = Info(
     description=' ZeroMQ',
     default_path=join(QP_ROOT_LIB, "libzmq.a"))
 
+gmp= Info(
+    url='https://gmplib.org/download/gmp/gmp-6.1.2.tar.bz2',
+    description=' The GNU Multiple Precision Arithmetic Library',
+    default_path=join(QP_ROOT_LIB, "libgmp.a"))
+
 f77zmq = Info(
     url='{head}/zeromq/f77_zmq/{tail}'.format(**path_github),
     description=' F77-ZeroMQ',
@@ -155,7 +161,7 @@ d_info = dict()
 
 for m in ["ocaml", "m4", "curl", "zlib", "patch", "irpf90", "docopt",
           "resultsFile", "ninja", "emsl", "ezfio", "p_graphviz",
-          "zeromq", "f77zmq", "bats"]: 
+          "zeromq", "f77zmq", "bats", "gmp"]: 
     exec ("d_info['{0}']={0}".format(m))
 
 
@@ -480,16 +486,16 @@ def create_ninja_and_rc(l_installed):
         'export QP_PYTHON={0}'.format(":".join(l_python)), "",
         'export IRPF90={0}'.format(path_irpf90.replace(QP_ROOT,"${QP_ROOT}")),
         'export NINJA={0}'.format(path_ninja.replace(QP_ROOT,"${QP_ROOT}")),
-        'function qp_append_export () {',
+        'function qp_prepend_export () {',
-        '  #Append path $2:${!1}. Add the semicolon only if ${!1} is defined',
+        '  #Prepend path $2:${!1}. Add the semicolon only if ${!1} is defined',
         '  eval "value_1=\"\${$1}\""',
-        '  echo ${2}${value_1:+:${value_1}}',
+        '  echo ${value_1:+${value_1}:}${2}',
         '}',
-        'export PYTHONPATH=$(qp_append_export "PYTHONPATH" "${QP_EZFIO}/Python":"${QP_PYTHON}")',
+        'export PYTHONPATH=$(qp_prepend_export "PYTHONPATH" "${QP_EZFIO}/Python":"${QP_PYTHON}")',
-        'export PATH=$(qp_append_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml)',
+        'export PATH=$(qp_prepend_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml)',
-        'export LD_LIBRARY_PATH=$(qp_append_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)',
+        'export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)',
-        'export LIBRARY_PATH=$(qp_append_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)',
+        'export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)',
-        'export C_INCLUDE_PATH=$(qp_append_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)',
+        'export C_INCLUDE_PATH=$(qp_prepend_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)',
         '',
         'if [[ $SHELL == "bash" ]] ; then',
         '  source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh',

install/scripts/install_ocaml.sh

@@ -5,11 +5,12 @@ QP_ROOT=$PWD
 cd -
 
 # Normal installation
-PACKAGES="core.v0.9.1 cryptokit.1.10 ocamlfind sexplib.v0.9.1 ZMQ ppx_sexp_conv ppx_deriving"
+PACKAGES="core.v0.10.0 cryptokit ocamlfind sexplib.v0.10.0 ZMQ ppx_sexp_conv ppx_deriving"
 
 # Needed for ZeroMQ
 export C_INCLUDE_PATH="${QP_ROOT}"/include:"${C_INCLUDE_PATH}"
 export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"
+export LDFLAGS="-L$QP_ROOT/lib"
 export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"
 
 # return 0 if program version is equal or greater than check version
@@ -64,7 +65,7 @@ fi
 cd Downloads || exit 1
 chmod +x  ocaml.sh || exit 1
 
-echo N | ./ocaml.sh ${QP_ROOT}/bin/ 4.04.2 || exit 1
+echo N | ./ocaml.sh ${QP_ROOT}/bin/ 4.06.0 || exit 1
 
 ${QP_ROOT}/bin/opam config setup -a -q || exit 1
 

ocaml/TaskServer.ml

@@ -1,6 +1,7 @@
 open Core
 open Qptypes
 
+module StringHashtbl = Hashtbl.Make(String)
 
 type pub_state =
 | Waiting
@@ -28,7 +29,7 @@ type t =
     progress_bar      : Progress_bar.t option ;
     running           : bool;
     accepting_clients : bool;
-    data              : (string, string) Hashtbl.t;
+    data              : string StringHashtbl.t;
 }
 
 
@@ -208,7 +209,7 @@ let end_job msg program_state rep_socket pair_socket =
           address_inproc    = None;
           running           = true;
           accepting_clients = false;
-          data = Hashtbl.create ~hashable:String.hashable ();
+          data = StringHashtbl.create ();
         }
 
     and wait n =
@@ -592,7 +593,7 @@ let put_data msg rest_of_msg program_state rep_socket =
     in
 
     let success ()  =
-      Hashtbl.set program_state.data ~key ~data:value ;
+      StringHashtbl.set program_state.data ~key ~data:value ;
       Message.PutDataReply (Message.PutDataReply_msg.create ())
       |> Message.to_string
       |> ZMQ.Socket.send rep_socket;
@@ -622,7 +623,7 @@ let get_data msg program_state rep_socket =
 
     let success () = 
       let value = 
-        match Hashtbl.find program_state.data key with
+        match StringHashtbl.find program_state.data key with
         | Some value -> value
         | None -> ""
       in
@@ -776,7 +777,7 @@ let run ~port =
         address_inproc = None;
         progress_bar = None ;
         accepting_clients = false;
-        data = Hashtbl.create ~hashable:String.hashable ();
+        data = StringHashtbl.create ();
     }
     in
 

ocaml/qp_create_ezfio_from_xyz.ml

@@ -665,7 +665,7 @@ let run ?o b au c d m p cart xyz_file =
 
 
 let command = 
-    Command.basic 
+    Command.basic_spec
     ~summary: "Quantum Package command"
     ~readme:(fun () -> "
 

ocaml/qp_create_guess.ml

@@ -128,7 +128,7 @@ let spec =
   +> anon ("ezfio_file" %: string)
 
 let () = 
-  Command.basic
+  Command.basic_spec
   ~summary: "Quantum Package command"
   ~readme:( fun () -> "
 Creates an open-shell multiplet initial guess\n\n" )

ocaml/qp_find_pi_space.ml

@@ -95,7 +95,7 @@ let spec =
 
 
 let command =
-    Command.basic
+    Command.basic_spec
     ~summary: "Quantum Package command"
     ~readme:(fun () ->
      "Find all the pi molecular orbitals to create a pi space.

ocaml/qp_print.ml

@@ -141,7 +141,7 @@ let run_o ~action ezfio_filename =
 ;;
 
 let command = 
-    Command.basic 
+    Command.basic_spec
     ~summary: "Quantum Package command"
     ~readme:(fun () ->
       "

ocaml/qp_run.ml

@@ -150,7 +150,7 @@ let spec =
 
 
 let () =
-  Command.basic
+  Command.basic_spec
   ~summary: "Quantum Package command"
   ~readme:( fun () -> "
 Executes a Quantum Package binary file among these:\n\n"

ocaml/qp_set_mo_class.ml

@@ -323,7 +323,7 @@ let spec =
 
 
 let command = 
-    Command.basic 
+    Command.basic_spec
     ~summary: "Quantum Package command"
     ~readme:(fun () ->
      "Set the orbital classes in an EZFIO directory

plugins/GPI2/NEEDED_CHILDREN_MODULES

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

plugins/GPI2/README.rst

@@ -1,14 +0,0 @@
-=====
-GASPI
-=====
-
-Providers for GASPI programs (with the GPI2 library).
-
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.

plugins/GPI2/gpi_test.irp.f

@@ -1,13 +0,0 @@
-program test
-  double precision :: energy(N_states)
-  if (is_gaspi_master) then
-    energy = 1.d0
-  else
-    energy = 0.d0
-  endif
-  call broadcast_wf(energy)
-  print *,  'energy (1.d0) :', GASPI_rank, energy(1)
-  print *,  'coef          :', GASPI_rank, psi_coef(1,1)
-  print *,  'det           :', GASPI_rank, psi_det (1,1,1)
-  call gaspi_finalize
-end

plugins/GPI2/utils.irp.f

@@ -1,76 +0,0 @@
- BEGIN_PROVIDER [ logical, GASPI_is_initialized ]
-&BEGIN_PROVIDER [ logical, has_gaspi ]
-  implicit none
-  BEGIN_DOC
-! This is true when GASPI_Init has been called
-  END_DOC
-
-  has_gaspi = .False.
-  IRP_IF GASPI
-      use GASPI
-      integer(gaspi_return_t) :: res
-      res = gaspi_proc_init(GASPI_BLOCK)
-      if (res /= GASPI_SUCCESS) then
-         print *, res
-         print *, 'GASPI failed to initialize'
-         stop -1
-      endif
-      has_gaspi = .True.
-  IRP_ENDIF
-  GASPI_is_initialized = .True.
-END_PROVIDER
-
-
- BEGIN_PROVIDER [ integer, GASPI_rank ]
-&BEGIN_PROVIDER [ integer, GASPI_size ]
-&BEGIN_PROVIDER [ logical, is_GASPI_master ]
- implicit none
- BEGIN_DOC
-! Usual GASPI variables
- END_DOC
-
- PROVIDE GASPI_is_initialized
-
- IRP_IF GASPI
-   use GASPI
-   integer(gaspi_return_t) :: res 
-   integer(gaspi_rank_t)   :: n
-   res = gaspi_proc_num(n)
-   GASPI_size = n
-   if (res  /= GASPI_SUCCESS) then
-     print *, res 
-     print *, 'Unable to get GASPI_size'
-     stop -1
-   endif
-   res = gaspi_proc_rank(n)
-   GASPI_rank = n
-   if (res  /= GASPI_SUCCESS) then
-     print *, res 
-     print *, 'Unable to get GASPI_rank'
-     stop -1
-   endif
-   is_GASPI_master = (GASPI_rank == 0)
- IRP_ELSE
-   GASPI_rank = 0
-   GASPI_size = 1
-   is_GASPI_master = .True.
- IRP_ENDIF
-
-
-END_PROVIDER
-
-subroutine gaspi_finalize()
-  implicit none
-  PROVIDE GASPI_is_initialized
-  IRP_IF GASPI
-    use GASPI
-    integer(gaspi_return_t) :: res 
-    res = gaspi_proc_term(GASPI_BLOCK)
-    if (res  /= GASPI_SUCCESS) then
-      print *, res 
-      print *, 'Unable to finalize GASPI'
-      stop -1
-    endif
-  IRP_ENDIF
-end subroutine
-

plugins/read_integral/NEEDED_CHILDREN_MODULES

@@ -1 +1 @@
-Integrals_Monoelec Integrals_Bielec
+Integrals_Monoelec Integrals_Bielec Hartree_Fock

plugins/read_integral/print_integrals_mo.irp.f

@@ -44,14 +44,12 @@ program print_integrals
   do l=1,mo_tot_num
    do k=1,mo_tot_num
     do j=l,mo_tot_num
-     do i=k,mo_tot_num
+     do i=max(j,k),mo_tot_num
-       !if (i>=j) then
+        double precision :: get_mo_bielec_integral
-          double precision :: get_mo_bielec_integral
+        integral = get_mo_bielec_integral(i,j,k,l,mo_integrals_map)
-          integral = get_mo_bielec_integral(i,j,k,l,mo_integrals_map)
+        if (dabs(integral) > mo_integrals_threshold) then
-          if (dabs(integral) > mo_integrals_threshold) then
+          write (iunit,'(4(I6,X),E25.15)') i,j,k,l, integral 
-            write (iunit,'(4(I6,X),F20.15)') i,j,k,l, integral 
+        endif
-          endif
-       !end if
      enddo
     enddo
    enddo

plugins/read_integral/read_integrals_mo.irp.f

@@ -5,8 +5,44 @@ program read_integrals
 ! - nuclear_mo
 ! - bielec_mo
   END_DOC
+
+  integer :: iunit
+  integer :: getunitandopen
+  integer :: i,j,n
+
   PROVIDE ezfio_filename
   call ezfio_set_integrals_monoelec_disk_access_mo_one_integrals("None")
+
+  logical :: has
+  call ezfio_has_mo_basis_mo_tot_num(has)
+  if (.not.has) then
+
+    iunit = getunitandopen('nuclear_mo','r')
+    n=0
+    do 
+      read (iunit,*,end=12) i
+      n = max(n,i)
+    enddo
+    12 continue
+    close(iunit)
+    call ezfio_set_mo_basis_mo_tot_num(n)
+
+    call ezfio_has_ao_basis_ao_num(has)
+    mo_label = "None"
+    if (has) then
+      call huckel_guess
+    else
+      call ezfio_set_ao_basis_ao_num(n)
+      double precision, allocatable :: X(:,:)
+      allocate (X(n,n))
+      X = 0.d0
+      do i=1,n
+        X(i,i) = 1.d0
+      enddo
+      call ezfio_set_mo_basis_mo_coef(X)
+      call save_mos
+    endif
+  endif
   call run
 end
 
@@ -69,9 +105,10 @@ subroutine run
   13 continue
   close(iunit)
   
-  call insert_into_mo_integrals_map(n_integrals,buffer_i,buffer_values,0.d0)
+  call map_append(mo_integrals_map, buffer_i, buffer_values, n_integrals)
 
   call map_sort(mo_integrals_map)
+  call map_unique(mo_integrals_map)
 
   call map_save_to_disk(trim(ezfio_filename)//'/work/mo_ints',mo_integrals_map)
   call ezfio_set_integrals_bielec_disk_access_mo_integrals("Read")

scripts/ezfio_interface/qp_edit_template

@@ -256,7 +256,7 @@ let spec =
 
 
 let command = 
-    Command.basic 
+    Command.basic_spec
     ~summary: "Quantum Package command"
     ~readme:(fun () ->
       "

scripts/ezfio_interface/upgrade_1.0_2.0.sh

@@ -1,27 +0,0 @@
-#!/bin/bash
-#  Convert a old ezfio file (with option.irp.f ezfio_default)
-# into a new EZFIO.cfg type
-
-# Hartree Fock
-# Changin the case, don't know if is needed or not 
-mv $1/Hartree_Fock $1/hartree_fock 2> /dev/null
-
-mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null
-
-# BiInts
-mv $1/bi_integrals $1/bielect_integrals 2> /dev/null
-
-if [ -f  $1/bielect_integrals/read_ao_integrals ]; then
-    if [ `cat $1/bielect_integrals/read_ao_integrals` -eq "True" ]
-    then
-            echo "Read" > $1/bielect_integrals/disk_access_ao_integrals
-    
-    elif [ `cat bielect_integrals/write_ao_integrals` -eq "True" ]
-    then
-            echo "Write" > $1/bielect_integrals/disk_access_ao_integrals
-    
-    else
-            echo "None" > $1/bielect_integrals/disk_access_ao_integrals
-    
-    fi
-fi

scripts/qp_upgrade_ocaml.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+OCAML_VERSION="4.06.0"
+PACKAGES="core.v0.10.0 cryptokit ocamlfind sexplib.v0.10.0 ZMQ ppx_sexp_conv ppx_deriving"
+
+if [[ -z ${QP_ROOT} ]]
+then
+  print "The QP_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+
+cd $QP_ROOT/ocaml
+opam update
+opam switch ${OCAML_VERSION}
+eval `opam config env`
+opam install -y ${PACKAGES} || echo "Upgrade failed. You can try running
+configure ; $0"
+