From 3967b197fa0ab8cbce39584b4e70ac6d0bd78e35 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 3 Jul 2019 08:29:59 +0200
Subject: [PATCH 01/21] Biblio

---
 docs/source/research.bib | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/docs/source/research.bib b/docs/source/research.bib
index 67a40766..124e1539 100644
--- a/docs/source/research.bib
+++ b/docs/source/research.bib
@@ -1,4 +1,14 @@
 %%% ARXIV TO BE UPDATED %%%
+@article{Giner2019Jul,
+        author = {Giner, Emmanuel and Scemama, Anthony and Toulouse, Julien and Loos, Pierre-Fran{\ifmmode\mbox{\c{c}}\else\c{c}\fi}ois},
+        title = {{Chemically Accurate Excitation Energies With Small Basis Sets}},
+        journal = {arXiv},
+        year = {2019},
+        month = {Jul},
+        eprint = {1907.01245},
+        url = {https://arxiv.org/abs/1907.01245}
+}
+
 @article{Dash2019May,
         author = {Dash, Monika and Feldt, Jonas and Moroni, Saverio and Scemama, Anthony and Filippi, Claudia},
         title = {{Excited states with selected CI-QMC: chemically accurate excitation energies and geometries}},

From 3763767f778aa7abef876e34959a234adf178532 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Tue, 9 Jul 2019 13:40:06 +0200
Subject: [PATCH 02/21] Fix bug with deterministic PT2

---
 src/cipsi/run_pt2_slave.irp.f       |  2 +-
 src/cipsi/run_selection_slave.irp.f | 72 +++++++++++++++--------------
 src/cipsi/slave_cipsi.irp.f         |  2 +-
 src/ezfio_files/ezfio.irp.f         |  2 +
 src/fci/pt2.irp.f                   |  9 +++-
 src/utils/c_functions.f90           | 19 ++++++++
 src/utils/memory.irp.f              |  3 ++
 src/zmq/utils.irp.f                 |  1 -
 8 files changed, 70 insertions(+), 40 deletions(-)
 create mode 100644 src/utils/c_functions.f90

diff --git a/src/cipsi/run_pt2_slave.irp.f b/src/cipsi/run_pt2_slave.irp.f
index 21def8f2..cb1bc83f 100644
--- a/src/cipsi/run_pt2_slave.irp.f
+++ b/src/cipsi/run_pt2_slave.irp.f
@@ -148,7 +148,7 @@ subroutine run_pt2_slave_small(thread,iproc,energy)
   integer, external :: disconnect_from_taskserver
   do i=1,300
     if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) /= -2) exit
-    call sleep(1)
+    call usleep(500)
     print *,  'Retry disconnect...'
   end do
 
diff --git a/src/cipsi/run_selection_slave.irp.f b/src/cipsi/run_selection_slave.irp.f
index c1542445..ac889794 100644
--- a/src/cipsi/run_selection_slave.irp.f
+++ b/src/cipsi/run_selection_slave.irp.f
@@ -74,7 +74,7 @@ subroutine run_selection_slave(thread,iproc,energy)
     if(done .or. ctask == size(task_id)) then
       do i=1, ctask
          if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id(i)) == -1) then
-           call sleep(1)
+           call usleep(100)
           if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id(i)) == -1) then
             ctask = 0
             done = .true.
@@ -85,6 +85,7 @@ subroutine run_selection_slave(thread,iproc,energy)
       if(ctask > 0) then
         call sort_selection_buffer(buf)
 !        call merge_selection_buffers(buf,buf2)
+print *, task_id(1), pt2(1), buf%cur, ctask
         call push_selection_results(zmq_socket_push, pt2, variance, norm, buf, task_id(1), ctask)
 !        buf%mini = buf2%mini
         pt2(:) = 0d0
@@ -132,23 +133,24 @@ subroutine push_selection_results(zmq_socket_push, pt2, variance, norm, b, task_
     print *,  'f77_zmq_send( zmq_socket_push, b%cur, 4, ZMQ_SNDMORE)'
   endif
 
+
+  rc = f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)
+  if(rc /= 8*N_states) then
+    print *,  'f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)'
+  endif
+
+  rc = f77_zmq_send( zmq_socket_push, variance, 8*N_states, ZMQ_SNDMORE)
+  if(rc /= 8*N_states) then
+    print *,  'f77_zmq_send( zmq_socket_push, variance, 8*N_states, ZMQ_SNDMORE)'
+  endif
+
+  rc = f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)
+  if(rc /= 8*N_states) then
+    print *,  'f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)'
+  endif
+
   if (b%cur > 0) then
 
-      rc = f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)
-      if(rc /= 8*N_states) then
-        print *,  'f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)'
-      endif
-
-      rc = f77_zmq_send( zmq_socket_push, variance, 8*N_states, ZMQ_SNDMORE)
-      if(rc /= 8*N_states) then
-        print *,  'f77_zmq_send( zmq_socket_push, variance, 8*N_states, ZMQ_SNDMORE)'
-      endif
-
-      rc = f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)
-      if(rc /= 8*N_states) then
-        print *,  'f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)'
-      endif
-
       rc = f77_zmq_send( zmq_socket_push, b%val(1), 8*b%cur, ZMQ_SNDMORE)
       if(rc /= 8*b%cur) then
         print *,  'f77_zmq_send( zmq_socket_push, b%val(1), 8*b%cur, ZMQ_SNDMORE)'
@@ -203,22 +205,26 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
     print *,  'f77_zmq_recv( zmq_socket_pull, N, 4, 0)'
   endif
 
+  pt2(:) = 0.d0
+  variance(:) = 0.d0
+  norm(:) = 0.d0
+
+  rc = f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)
+  if(rc /= 8*N_states) then
+    print *,  'f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)'
+  endif
+
+  rc = f77_zmq_recv( zmq_socket_pull, variance, N_states*8, 0)
+  if(rc /= 8*N_states) then
+    print *,  'f77_zmq_recv( zmq_socket_pull, variance, N_states*8, 0)'
+  endif
+
+  rc = f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)
+  if(rc /= 8*N_states) then
+    print *,  'f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)'
+  endif
+
   if (N>0) then
-      rc = f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)
-      if(rc /= 8*N_states) then
-        print *,  'f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)'
-      endif
-
-      rc = f77_zmq_recv( zmq_socket_pull, variance, N_states*8, 0)
-      if(rc /= 8*N_states) then
-        print *,  'f77_zmq_recv( zmq_socket_pull, variance, N_states*8, 0)'
-      endif
-
-      rc = f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)
-      if(rc /= 8*N_states) then
-        print *,  'f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)'
-      endif
-
       rc = f77_zmq_recv( zmq_socket_pull, val(1), 8*N, 0)
       if(rc /= 8*N) then
         print *,  'f77_zmq_recv( zmq_socket_pull, val(1), 8*N, 0)'
@@ -228,10 +234,6 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
       if(rc /= bit_kind*N_int*2*N) then
         print *,  'f77_zmq_recv( zmq_socket_pull, det(1,1,1), bit_kind*N_int*2*N, 0)'
       endif
-  else
-      pt2(:) = 0.d0
-      variance(:) = 0.d0
-      norm(:) = 0.d0
   endif
 
   rc = f77_zmq_recv( zmq_socket_pull, ntask, 4, 0)
diff --git a/src/cipsi/slave_cipsi.irp.f b/src/cipsi/slave_cipsi.irp.f
index c9710c18..3e33dfa8 100644
--- a/src/cipsi/slave_cipsi.irp.f
+++ b/src/cipsi/slave_cipsi.irp.f
@@ -63,7 +63,7 @@ subroutine run_slave_main
     if (mpi_master) then
       call wait_for_states(states,zmq_state,size(states))
       if (zmq_state(1:64) == old_state(1:64)) then
-        call sleep(1)
+        call usleep(200)
         cycle
       else
         old_state(1:64) = zmq_state(1:64)
diff --git a/src/ezfio_files/ezfio.irp.f b/src/ezfio_files/ezfio.irp.f
index 70277992..e7a7a159 100644
--- a/src/ezfio_files/ezfio.irp.f
+++ b/src/ezfio_files/ezfio.irp.f
@@ -39,6 +39,8 @@ BEGIN_PROVIDER [ character*(128), ezfio_filename ]
   write(command,*) 'echo 15 > /proc//'//trim(adjustl(pidc))//'/oom_adj'
   call system(command)
 
+  PROVIDE file_lock
+
 END_PROVIDER
 
 BEGIN_PROVIDER [ character*(128), ezfio_work_dir ]
diff --git a/src/fci/pt2.irp.f b/src/fci/pt2.irp.f
index 6135864f..c916e0ef 100644
--- a/src/fci/pt2.irp.f
+++ b/src/fci/pt2.irp.f
@@ -43,8 +43,13 @@ subroutine run
   E_CI_before(:) = psi_energy(:) + nuclear_repulsion
   relative_error=PT2_relative_error
 
-  call ZMQ_pt2(psi_energy_with_nucl_rep,pt2,relative_error,error, variance, &
-     norm,0) ! Stochastic PT2
+  if (do_pt2) then
+    call ZMQ_pt2(psi_energy_with_nucl_rep,pt2,relative_error,error, variance, &
+      norm,0) ! Stochastic PT2
+  else
+    call ZMQ_selection(0, pt2, variance, norm)
+  endif
+
   do k=1,N_states
     rpt2(k) = pt2(k)/(1.d0 + norm(k))
   enddo
diff --git a/src/utils/c_functions.f90 b/src/utils/c_functions.f90
new file mode 100644
index 00000000..32bd5005
--- /dev/null
+++ b/src/utils/c_functions.f90
@@ -0,0 +1,19 @@
+module c_functions
+  use iso_c_binding
+
+  interface
+    subroutine usleep_c(us) bind (C,name="usleep")
+      use iso_c_binding
+      integer(c_int), value :: us
+    end subroutine usleep_c
+  end interface
+
+end module
+
+subroutine usleep(us)
+  use c_functions
+  use iso_c_binding
+  implicit none
+  integer, intent(in) :: us
+  call usleep_c(int(us,c_int))
+end
diff --git a/src/utils/memory.irp.f b/src/utils/memory.irp.f
index f9e4bb69..3e077f97 100644
--- a/src/utils/memory.irp.f
+++ b/src/utils/memory.irp.f
@@ -15,6 +15,7 @@ BEGIN_PROVIDER [ integer, qp_max_mem ]
 END_PROVIDER
 
 subroutine resident_memory(value)
+  use c_functions
   implicit none
   BEGIN_DOC
 ! Returns the current used memory in gigabytes used by the current process.
@@ -25,6 +26,8 @@ subroutine resident_memory(value)
   double precision, intent(out) :: value
 
   call omp_set_lock(file_lock)
+  call usleep(10)
+
   value = 0.d0
   iunit = getUnitAndOpen('/proc/self/status','r')
   do
diff --git a/src/zmq/utils.irp.f b/src/zmq/utils.irp.f
index 1205e09e..e936f268 100644
--- a/src/zmq/utils.irp.f
+++ b/src/zmq/utils.irp.f
@@ -275,7 +275,6 @@ IRP_ENDIF
     rc = f77_zmq_bind(new_zmq_pull_socket, zmq_socket_pull_tcp_address)
     if (rc /= 0) then
       icount = icount-1
-!      call sleep(3)
       zmq_socket_pull_tcp_address    = 'tcp://*:'//zmq_port(2+icount*100)//' '
       zmq_socket_push_tcp_address    = trim(qp_run_address)//':'//zmq_port(2+icount*100)//' '
     else

From e0b06889c81eb3806b459ab24a541f103d21a2e1 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Tue, 9 Jul 2019 17:15:30 +0200
Subject: [PATCH 03/21] Cleaning

---
 src/zmq/utils.irp.f | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/zmq/utils.irp.f b/src/zmq/utils.irp.f
index 70f0830b..b376c185 100644
--- a/src/zmq/utils.irp.f
+++ b/src/zmq/utils.irp.f
@@ -752,7 +752,8 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task)
 
   add_task_to_taskserver = 0
 
-  allocate(character(len=len(task)+10+len(zmq_state)) :: message)
+  sze = len(trim(task)) + len(trim(zmq_state))+11
+  allocate(character(len=sze) :: message)
   message='add_task '//trim(zmq_state)//' '//trim(task)
   sze = len(message)
   rc = f77_zmq_send(zmq_to_qp_run_socket, message, sze, 0)
@@ -768,6 +769,7 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task)
     add_task_to_taskserver = -1
     return
   endif
+  deallocate(message)
 
 end
 

From 1120d572fa82034cedbf193c0b7d0cc8c3fc954a Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Tue, 9 Jul 2019 17:18:05 +0200
Subject: [PATCH 04/21] Cleaning allocation of string

---
 src/utils/c_functions.f90 |  4 +++-
 src/zmq/utils.irp.f       | 10 ++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/utils/c_functions.f90 b/src/utils/c_functions.f90
index 32bd5005..52c01d12 100644
--- a/src/utils/c_functions.f90
+++ b/src/utils/c_functions.f90
@@ -15,5 +15,7 @@ subroutine usleep(us)
   use iso_c_binding
   implicit none
   integer, intent(in) :: us
-  call usleep_c(int(us,c_int))
+  integer(c_int) :: u
+  u = us
+  call usleep_c(u)
 end
diff --git a/src/zmq/utils.irp.f b/src/zmq/utils.irp.f
index e936f268..e76238ed 100644
--- a/src/zmq/utils.irp.f
+++ b/src/zmq/utils.irp.f
@@ -300,7 +300,6 @@ function new_zmq_push_socket(thread)
   END_DOC
   integer, intent(in)            :: thread
   integer                        :: rc
-  character*(8), external        :: zmq_port
   integer(ZMQ_PTR)               :: new_zmq_push_socket
 
   call omp_set_lock(zmq_lock)
@@ -424,7 +423,6 @@ subroutine end_zmq_pair_socket(zmq_socket_pair)
   END_DOC
   integer(ZMQ_PTR), intent(in)   :: zmq_socket_pair
   integer                        :: rc
-  character*(8), external        :: zmq_port
 
   call omp_set_lock(zmq_lock)
   rc = f77_zmq_close(zmq_socket_pair)
@@ -444,7 +442,6 @@ subroutine end_zmq_pull_socket(zmq_socket_pull)
   END_DOC
   integer(ZMQ_PTR), intent(in)   :: zmq_socket_pull
   integer                        :: rc
-  character*(8), external        :: zmq_port
 
 !  rc = f77_zmq_setsockopt(zmq_socket_pull,ZMQ_LINGER,0,4)
 !  if (rc /= 0) then
@@ -471,7 +468,6 @@ subroutine end_zmq_push_socket(zmq_socket_push,thread)
   integer, intent(in)            :: thread
   integer(ZMQ_PTR), intent(in)   :: zmq_socket_push
   integer                        :: rc
-  character*(8), external        :: zmq_port
 
   rc = f77_zmq_setsockopt(zmq_socket_push,ZMQ_LINGER,300000,4)
   if (rc /= 0) then
@@ -751,10 +747,12 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task)
   character*(*), intent(in)      :: task
 
   integer                        :: rc, sze
-  character(len=:), allocatable :: message
+  character(len=:), allocatable  :: message
 
   add_task_to_taskserver = 0
 
+  sze = len(trim(task)) + len(trim(zmq_state))+11
+  allocate(character(len=sze) :: message)
   message='add_task '//trim(zmq_state)//' '//trim(task)
   sze = len(message)
   rc = f77_zmq_send(zmq_to_qp_run_socket, message, sze, 0)
@@ -770,6 +768,7 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task)
     add_task_to_taskserver = -1
     return
   endif
+  deallocate(message)
 
 end
 
@@ -1031,7 +1030,6 @@ subroutine end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
 ! Terminate the socket from the application to qp_run
   END_DOC
   integer(ZMQ_PTR), intent(in)   :: zmq_to_qp_run_socket
-  character*(8), external        :: zmq_port
   integer                        :: rc
 
   rc = f77_zmq_setsockopt(zmq_to_qp_run_socket,ZMQ_LINGER,300000,4)

From edd2276b75fb24a54e36ff86bce8f72a0ba98597 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Tue, 9 Jul 2019 17:33:44 +0200
Subject: [PATCH 05/21] Fixed usleep

---
 src/utils/c_funcs.c       | 6 ++++++
 src/utils/c_functions.f90 | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)
 create mode 100644 src/utils/c_funcs.c

diff --git a/src/utils/c_funcs.c b/src/utils/c_funcs.c
new file mode 100644
index 00000000..5b7035fb
--- /dev/null
+++ b/src/utils/c_funcs.c
@@ -0,0 +1,6 @@
+#include <unistd.h>
+
+void usleep_c(int s)
+{
+  usleep((useconds_t) s);
+}
diff --git a/src/utils/c_functions.f90 b/src/utils/c_functions.f90
index 52c01d12..425aafd6 100644
--- a/src/utils/c_functions.f90
+++ b/src/utils/c_functions.f90
@@ -2,7 +2,7 @@ module c_functions
   use iso_c_binding
 
   interface
-    subroutine usleep_c(us) bind (C,name="usleep")
+    subroutine usleep_c(us) bind (C,name="usleep_c")
       use iso_c_binding
       integer(c_int), value :: us
     end subroutine usleep_c

From bf96d8c0c898cdffab2423eb39e470924659d960 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Tue, 23 Jul 2019 14:54:03 +0200
Subject: [PATCH 06/21] Renamed disk_access_nuclear_repulsion

---
 REPLACE                      | 1 +
 src/ao_one_e_ints/README.rst | 7 +++----
 src/nuclei/EZFIO.cfg         | 2 +-
 src/nuclei/nuclei.irp.f      | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/REPLACE b/REPLACE
index 10a53958..d0b6adce 100755
--- a/REPLACE
+++ b/REPLACE
@@ -834,3 +834,4 @@ qp_name potential_sr_c_alpha_ao_pbe --rename=potential_c_alpha_ao_sr_pbe
 qp_name potential_sr_c_beta_ao_pbe --rename=potential_c_beta_ao_sr_pbe
 qp_name potential_sr_xc_alpha_ao_pbe --rename=potential_xc_alpha_ao_sr_pbe
 qp_name potential_sr_xc_beta_ao_pbe --rename=potential_xc_beta_ao_sr_pbe
+qp_name disk_access_nuclear_repulsion --rename=io_nuclear_repulsion
diff --git a/src/ao_one_e_ints/README.rst b/src/ao_one_e_ints/README.rst
index bc8832c3..a87bdb17 100644
--- a/src/ao_one_e_ints/README.rst
+++ b/src/ao_one_e_ints/README.rst
@@ -6,9 +6,8 @@ All the one-electron integrals in the |AO| basis are here.
 
 The most important providers for usual quantum-chemistry calculation are:
 
-* `ao_kinetic_integral` which are the kinetic operator integrals on the |AO| basis (see :file:`kin_ao_ints.irp.f`)
-* `ao_nucl_elec_integral` which are the nuclear-elctron operator integrals on the |AO| basis (see :file:`pot_ao_ints.irp.f`)
-* `ao_one_e_integrals` which are the the h_core operator integrals on the |AO| basis (see :file:`ao_mono_ints.irp.f`)
+* `ao_kinetic_integrals` which are the kinetic operator integrals on the |AO| basis 
+* `ao_integrals_n_e` which are the nuclear-elctron operator integrals on the |AO| basis
+* `ao_one_e_integrals` which are the the h_core operator integrals on the |AO| basis
 
 
-Note that you can find other interesting integrals related to the position operator in :file:`spread_dipole_ao.irp.f`.
diff --git a/src/nuclei/EZFIO.cfg b/src/nuclei/EZFIO.cfg
index 7bcbf013..ebdcfead 100644
--- a/src/nuclei/EZFIO.cfg
+++ b/src/nuclei/EZFIO.cfg
@@ -21,7 +21,7 @@ type: double precision
 size: (nuclei.nucl_num,3)
 interface: ezfio
 
-[disk_access_nuclear_repulsion]
+[io_nuclear_repulsion]
 doc: Read/Write Nuclear Repulsion from/to disk [ Write | Read | None ]
 type: Disk_access
 interface: ezfio,provider,ocaml
diff --git a/src/nuclei/nuclei.irp.f b/src/nuclei/nuclei.irp.f
index c797ff30..88ee24e8 100644
--- a/src/nuclei/nuclei.irp.f
+++ b/src/nuclei/nuclei.irp.f
@@ -143,7 +143,7 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ]
    END_DOC
 
    PROVIDE mpi_master nucl_coord nucl_charge nucl_num
-   if (disk_access_nuclear_repulsion.EQ.'Read') then
+   if (io_nuclear_repulsion == 'Read') then
      logical                        :: has
 
      if (mpi_master) then
@@ -194,7 +194,7 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ]
    call write_time(6)
    call write_double(6,nuclear_repulsion,'Nuclear repulsion energy')
 
-   if (disk_access_nuclear_repulsion.EQ.'Write') then
+   if (io_nuclear_repulsion == 'Write') then
      if (mpi_master) then
        call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion)
      endif

From a8dbea61d3d542089fb61c7392b5060508735d33 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 24 Jul 2019 08:11:17 +0200
Subject: [PATCH 07/21] Fixed opam installation

---
 INSTALL.rst | 11 +++++++++--
 configure   |  6 ++++--
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/INSTALL.rst b/INSTALL.rst
index c91b184f..10f583db 100644
--- a/INSTALL.rst
+++ b/INSTALL.rst
@@ -328,7 +328,7 @@ OCaml
      echo ${QP_ROOT}/bin
      ${QP_ROOT}/external/opam_installer.sh --no-backup --fresh
 
-  You the :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin`
+  The :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin`
   directory. To do this, take the output of ``echo ${QP_ROOT}/bin`` and
   use it as an answer to where :command:`opam` should be installed.
   
@@ -337,7 +337,14 @@ OCaml
 
   .. code:: bash
 
-      opam init --disable-sandboxing --comp=4.07.0
+      opam init --comp=4.07.1
+      eval `${QP_ROOT}/bin/opam env`
+
+  If the installation fails because of bwrap, the you can initialize opam using:
+
+  .. code:: bash
+
+      opam init --disable-sandboxing --comp=4.07.1
       eval `${QP_ROOT}/bin/opam env`
 
 * Install the required external OCaml libraries
diff --git a/configure b/configure
index c343c243..c3ff8942 100755
--- a/configure
+++ b/configure
@@ -297,12 +297,13 @@ EOF
 ${QP_ROOT}/bin
 
 
+
 EOF
 
                 rm ${QP_ROOT}/external/opam_installer.sh
                 source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
 
-                ${QP_ROOT}/bin/opam init --verbose --yes 
+                ${QP_ROOT}/bin/opam init --verbose --yes --comp=4.07.1 --disable-sandboxing
 
                 eval $(${QP_ROOT}/bin/opam env)
                 opam install -y ${OCAML_PACKAGES}  || exit 1
@@ -310,13 +311,14 @@ EOF
                 # Conventional commands
                 execute << EOF
                   chmod +x "\${QP_ROOT}"/external/opam_installer.sh
+                  "\${QP_ROOT}"/external/opam_installer.sh --no-backup 
                   rm --force \${QP_ROOT}/bin/opam
                   export OPAMROOT=\${OPAMROOT:-\${QP_ROOT}/external/opam}
                   echo \${QP_ROOT}/bin \
                   | sh \${QP_ROOT}/external/opam_installer.sh 
                   rm \${QP_ROOT}/external/opam_installer.sh
                   source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
-                  \${QP_ROOT}/bin/opam init --verbose --yes
+                  \${QP_ROOT}/bin/opam init --verbose --yes --comp=4.07.1 --disable-sandboxing
                   eval \$(\${QP_ROOT}/bin/opam env)
                   opam install -y \${OCAML_PACKAGES}  || exit 1
 EOF

From 4e58fe7576b320c6c282762f3df538397f413aeb Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 24 Jul 2019 08:12:22 +0200
Subject: [PATCH 08/21] Typo

---
 INSTALL.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/INSTALL.rst b/INSTALL.rst
index 10f583db..a9cee40b 100644
--- a/INSTALL.rst
+++ b/INSTALL.rst
@@ -340,7 +340,7 @@ OCaml
       opam init --comp=4.07.1
       eval `${QP_ROOT}/bin/opam env`
 
-  If the installation fails because of bwrap, the you can initialize opam using:
+  If the installation fails because of bwrap, you can initialize opam using:
 
   .. code:: bash
 

From c405dc99d3cdd1c9ffa6afc6bb8f91758a1321e5 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 24 Jul 2019 09:06:11 +0200
Subject: [PATCH 09/21] Fixing travis

---
 configure | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/configure b/configure
index c3ff8942..634b5888 100755
--- a/configure
+++ b/configure
@@ -303,22 +303,30 @@ EOF
                 rm ${QP_ROOT}/external/opam_installer.sh
                 source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
 
-                ${QP_ROOT}/bin/opam init --verbose --yes --comp=4.07.1 --disable-sandboxing
+                execute << EOF
+                ${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
 
                 eval $(${QP_ROOT}/bin/opam env)
                 opam install -y ${OCAML_PACKAGES}  || exit 1
+EOF
             else
                 # Conventional commands
                 execute << EOF
                   chmod +x "\${QP_ROOT}"/external/opam_installer.sh
                   "\${QP_ROOT}"/external/opam_installer.sh --no-backup 
+EOF
+                execute << EOF
                   rm --force \${QP_ROOT}/bin/opam
                   export OPAMROOT=\${OPAMROOT:-\${QP_ROOT}/external/opam}
                   echo \${QP_ROOT}/bin \
                   | sh \${QP_ROOT}/external/opam_installer.sh 
+EOF
+                execute << EOF
                   rm \${QP_ROOT}/external/opam_installer.sh
                   source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
-                  \${QP_ROOT}/bin/opam init --verbose --yes --comp=4.07.1 --disable-sandboxing
+                  \${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
+EOF
+                execute << EOF
                   eval \$(\${QP_ROOT}/bin/opam env)
                   opam install -y \${OCAML_PACKAGES}  || exit 1
 EOF

From be6c9b533ead2710e12e69107a3edb705d2e6180 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 24 Jul 2019 09:36:51 +0200
Subject: [PATCH 10/21] Fixing travis

---
 configure | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/configure b/configure
index 634b5888..228b4f3f 100755
--- a/configure
+++ b/configure
@@ -304,6 +304,7 @@ EOF
                 source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
 
                 execute << EOF
+                opam switch 4.07.1  || exit 1
                 ${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
 
                 eval $(${QP_ROOT}/bin/opam env)
@@ -324,6 +325,7 @@ EOF
                 execute << EOF
                   rm \${QP_ROOT}/external/opam_installer.sh
                   source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
+                  opam switch 4.07.1  || exit 1
                   \${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
 EOF
                 execute << EOF

From 00074558463e79e00bf130f4ae437d8a161d094c Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 24 Jul 2019 10:27:39 +0200
Subject: [PATCH 11/21] Fixing travis

---
 configure | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/configure b/configure
index 228b4f3f..e605c088 100755
--- a/configure
+++ b/configure
@@ -304,7 +304,7 @@ EOF
                 source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
 
                 execute << EOF
-                opam switch 4.07.1  || exit 1
+                opam switch create ocaml-base-compiler.4.07.1     || exit 1
                 ${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
 
                 eval $(${QP_ROOT}/bin/opam env)
@@ -325,7 +325,7 @@ EOF
                 execute << EOF
                   rm \${QP_ROOT}/external/opam_installer.sh
                   source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
-                  opam switch 4.07.1  || exit 1
+                  opam switch create ocaml-base-compiler.4.07.1     || exit 1
                   \${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
 EOF
                 execute << EOF

From 2f89be4ee9ec6c29d167b4b1021d33d90c5160c2 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 24 Jul 2019 12:33:08 +0200
Subject: [PATCH 12/21] Fixing travis

---
 configure | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/configure b/configure
index e605c088..98641633 100755
--- a/configure
+++ b/configure
@@ -303,13 +303,12 @@ EOF
                 rm ${QP_ROOT}/external/opam_installer.sh
                 source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
 
-                execute << EOF
-                opam switch create ocaml-base-compiler.4.07.1     || exit 1
-                ${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
+                opam switch create ocaml-base-compiler.4.07.1
+                opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
 
-                eval $(${QP_ROOT}/bin/opam env)
+                eval $(opam env)
                 opam install -y ${OCAML_PACKAGES}  || exit 1
-EOF
+
             else
                 # Conventional commands
                 execute << EOF
@@ -322,14 +321,13 @@ EOF
                   echo \${QP_ROOT}/bin \
                   | sh \${QP_ROOT}/external/opam_installer.sh 
 EOF
-                execute << EOF
-                  rm \${QP_ROOT}/external/opam_installer.sh
-                  source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
-                  opam switch create ocaml-base-compiler.4.07.1     || exit 1
-                  \${QP_ROOT}/bin/opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
+                rm \${QP_ROOT}/external/opam_installer.sh
+                source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
+                opam switch create ocaml-base-compiler.4.07.1     || exit 1
+                opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
+                eval $(opam env)
 EOF
                 execute << EOF
-                  eval \$(\${QP_ROOT}/bin/opam env)
                   opam install -y \${OCAML_PACKAGES}  || exit 1
 EOF
             fi

From 861aed9dd4c0a9c8fe2183a9892f68ec2f64b03c Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 24 Jul 2019 12:40:05 +0200
Subject: [PATCH 13/21] Update GITHUB.md

---
 GITHUB.md | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/GITHUB.md b/GITHUB.md
index 02836a37..cee4cc8c 100644
--- a/GITHUB.md
+++ b/GITHUB.md
@@ -2,20 +2,23 @@ GitHub Branches
 ===============
 
 master:
-  The current up-to-date working branch, that users download It should
-  only contain the latest release and bug fixes.
+  The current up-to-date working branch, that users download. It should
+  only contain the latest stable release and bug fixes.
 
-develop-lcpq:
-  Toulouse development branch  
-
-develop-lct:
-  Paris development branch  
-
-develop:
+dev:
   It is a fork of the *master* branch with new developments that will be
   merged in the *master* branch for the next release. Other development
   branches should be merged on this one.
 
+bugfix:
+  A fork of the *master* on which the bug fixes are made.
+
+dev-lcpq:
+  Toulouse development branch  
+
+dev-lct:
+  Paris development branch  
+
 gh-pages:
   This is an independent branch, containing only the web site of QP2.
 

From 2e86462070aff808cb15b50f6613a84f99cf7c55 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 24 Jul 2019 12:56:45 +0200
Subject: [PATCH 14/21] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e7fab0c9..3349f561 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 
 [*Quantum package 2.0: an open-source determinant-driven suite of programs*](https://pubs.acs.org/doi/10.1021/acs.jctc.9b00176)\
 Y. Garniron, K. Gasperich, T. Applencourt, A. Benali, A. Ferté, J. Paquier, B. Pradines, R. Assaraf, P. Reinhardt, J. Toulouse, P. Barbaresco, N. Renon, G. David, J. P. Malrieu, M. Véril, M. Caffarel, P. F. Loos, E. Giner and A. Scemama\
-J. Chem. Theory Comput., 15:6, 3591--3609, (2019)\
+[J. Chem. Theory Comput. 2019, 15, 6, 3591-3609](https://doi.org/10.1021/acs.jctc.9b00176)\
 https://arxiv.org/abs/1902.08154
 
 ```

From faaba29eb7a7c72b1eddd61a60107d8f457736e9 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Fri, 26 Jul 2019 12:39:58 +0200
Subject: [PATCH 15/21] Fix rm opam_installer.sh (#53)

* Changed native into SSE4.2 in gfortran.cfg

* Fixed rm opam_installer
---
 config/gfortran.cfg | 2 +-
 configure           | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/config/gfortran.cfg b/config/gfortran.cfg
index 94a12ccf..f561fcb7 100644
--- a/config/gfortran.cfg
+++ b/config/gfortran.cfg
@@ -35,7 +35,7 @@ OPENMP  : 1          ; Append OpenMP flags
 #                           -ffast-math and the Fortran-specific
 #                           -fno-protect-parens and -fstack-arrays.
 [OPT]
-FCFLAGS : -Ofast -march=native
+FCFLAGS : -Ofast -msse4.2
 
 # Profiling flags
 #################
diff --git a/configure b/configure
index 98641633..2599fbbc 100755
--- a/configure
+++ b/configure
@@ -321,8 +321,8 @@ EOF
                   echo \${QP_ROOT}/bin \
                   | sh \${QP_ROOT}/external/opam_installer.sh 
 EOF
-                rm \${QP_ROOT}/external/opam_installer.sh
-                source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
+                rm ${QP_ROOT}/external/opam_installer.sh
+                source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
                 opam switch create ocaml-base-compiler.4.07.1     || exit 1
                 opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
                 eval $(opam env)

From b65400c5442794f2b9deaaeb23cb5fa5122e9a26 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Mon, 19 Aug 2019 13:14:01 +0200
Subject: [PATCH 16/21] Update biblio (#55)

---
 docs/source/research.bib | 50 +++++++++++++++++++++++++++-------------
 1 file changed, 34 insertions(+), 16 deletions(-)

diff --git a/docs/source/research.bib b/docs/source/research.bib
index 124e1539..9e200698 100644
--- a/docs/source/research.bib
+++ b/docs/source/research.bib
@@ -9,29 +9,47 @@
         url = {https://arxiv.org/abs/1907.01245}
 }
 
-@article{Dash2019May,
-        author = {Dash, Monika and Feldt, Jonas and Moroni, Saverio and Scemama, Anthony and Filippi, Claudia},
-        title = {{Excited states with selected CI-QMC: chemically accurate excitation energies and geometries}},
-        journal = {arXiv},
-        year = {2019},
-        month = {May},
-        eprint = {1905.06737},
-        url = {https://arxiv.org/abs/1905.06737}
+
+@article{Burton_2019,
+        doi = {10.1021/acs.jctc.9b00441},
+        url = {https://doi.org/10.1021%2Facs.jctc.9b00441},
+        year = 2019,
+        month = {aug},
+        publisher = {American Chemical Society ({ACS})},
+        author = {Hugh G. A. Burton and Alex J.W. Thom},
+        title = {A General Approach for Multireference Ground and Excited States using Non-Orthogonal Configuration Interaction},
+        journal = {Journal of Chemical Theory and Computation}
 }
 
-@article{Burton2019May,
-        author = {Burton, Hugh G. A. and Thom, Alex J. W.},
-        title = {{A General Approach for Multireference Ground and Excited States using Non-Orthogonal Configuration Interaction}},
-        journal = {arXiv},
-        year = {2019},
-        month = {May},
-        eprint = {1905.02626},
-        url = {https://arxiv.org/abs/1905.02626}
+
+@article{Dash_2019,
+        doi = {10.1021/acs.jctc.9b00476},
+        url = {https://doi.org/10.1021%2Facs.jctc.9b00476},
+        year = 2019,
+        month = {aug},
+        publisher = {American Chemical Society ({ACS})},
+        author = {Monika Dash and Jonas Feldt and Saverio Moroni and Anthony Scemama and Claudia Filippi},
+        title = {Excited States with Selected Configuration Interaction-Quantum Monte Carlo: Chemically Accurate Excitation Energies and Geometries},
+        journal = {Journal of Chemical Theory and Computation}
 }
 
 
 
 %%%% PUBLISHED PAPERS
+@article{Caffarel_2019,
+        doi = {10.1063/1.5114703},
+        url = {https://doi.org/10.1063%2F1.5114703},
+        year = 2019,
+        month = {aug},
+        publisher = {{AIP} Publishing},
+        volume = {151},
+        number = {6},
+        pages = {064101},
+        author = {Michel Caffarel},
+        title = {Evaluating two-electron-repulsion integrals over arbitrary orbitals using zero variance Monte Carlo: Application to full configuration interaction calculations with Slater-type orbitals},
+        journal = {The Journal of Chemical Physics}
+}
+
 @article{Loos_2019,
         doi = {10.1021/acs.jpclett.9b01176},
         url = {https://doi.org/10.1021%2Facs.jpclett.9b01176},

From cd2b606daa5928131b784f14d72e127eb52a33a2 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Mon, 19 Aug 2019 18:57:43 +0200
Subject: [PATCH 17/21] Biblio (#57)

* Update biblio

* Update paper
---
 docs/source/research.bib | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/docs/source/research.bib b/docs/source/research.bib
index 9e200698..e6c75b9e 100644
--- a/docs/source/research.bib
+++ b/docs/source/research.bib
@@ -36,6 +36,19 @@
 
 
 %%%% PUBLISHED PAPERS
+@article{Ferte_2019,
+        doi = {10.1063/1.5082638},
+        url = {https://doi.org/10.1063%2F1.5082638},
+        year = 2019,
+        month = {feb},
+        publisher = {{AIP} Publishing},
+        volume = {150},
+        number = {8},
+        pages = {084103},
+        author = {Anthony Fert{\'{e}} and Emmanuel Giner and Julien Toulouse},
+        title = {Range-separated multideterminant density-functional theory with a short-range correlation functional of the on-top pair density},
+}
+
 @article{Caffarel_2019,
         doi = {10.1063/1.5114703},
         url = {https://doi.org/10.1063%2F1.5114703},

From fcade8c8f7a67f7ccd877a189cf36cf559e7540e Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Mon, 19 Aug 2019 20:11:39 +0200
Subject: [PATCH 18/21] Fixed installation issues with OPAM

* Changed native into SSE4.2 in gfortran.cfg

* Fixed rm opam_installer

* Fixing opam installation

* Introduce NO_CACHE in configure for daily test
---
 configure                | 26 +++++++++++++++-----------
 docs/source/research.bib |  2 +-
 2 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/configure b/configure
index 2599fbbc..23f4aa02 100755
--- a/configure
+++ b/configure
@@ -292,6 +292,9 @@ EOF
                 # Special commands for Travis CI
                 chmod +x "${QP_ROOT}"/external/opam_installer.sh
                 rm --force ${QP_ROOT}/bin/opam
+                if [[ -n ${NO_CACHE} ]] ; then
+                        rm -rf ${HOME}/.opam
+                fi
                 export OPAMROOT=${HOME}/.opam
                 cat << EOF | bash ${QP_ROOT}/external/opam_installer.sh --no-backup 
 ${QP_ROOT}/bin
@@ -301,9 +304,9 @@ ${QP_ROOT}/bin
 EOF
 
                 rm ${QP_ROOT}/external/opam_installer.sh
-                source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
-
-                opam switch create ocaml-base-compiler.4.07.1
+#                source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
+#
+#                opam switch create ocaml-base-compiler.4.07.1
                 opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
 
                 eval $(opam env)
@@ -312,18 +315,19 @@ EOF
             else
                 # Conventional commands
                 execute << EOF
-                  chmod +x "\${QP_ROOT}"/external/opam_installer.sh
-                  "\${QP_ROOT}"/external/opam_installer.sh --no-backup 
+                  chmod +x "${QP_ROOT}"/external/opam_installer.sh
+                  "${QP_ROOT}"/external/opam_installer.sh --no-backup 
 EOF
                 execute << EOF
-                  rm --force \${QP_ROOT}/bin/opam
-                  export OPAMROOT=\${OPAMROOT:-\${QP_ROOT}/external/opam}
-                  echo \${QP_ROOT}/bin \
-                  | sh \${QP_ROOT}/external/opam_installer.sh 
+                  rm --force ${QP_ROOT}/bin/opam
+                  export OPAMROOT=${OPAMROOT:-${QP_ROOT}/external/opam}
+                  echo ${QP_ROOT}/bin \
+                  | sh ${QP_ROOT}/external/opam_installer.sh 
 EOF
                 rm ${QP_ROOT}/external/opam_installer.sh
-                source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
-                opam switch create ocaml-base-compiler.4.07.1     || exit 1
+#                source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
+#                opam switch create ocaml-base-compiler.4.07.1     || exit 1
+
                 opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
                 eval $(opam env)
 EOF
diff --git a/docs/source/research.bib b/docs/source/research.bib
index e6c75b9e..f0c0648c 100644
--- a/docs/source/research.bib
+++ b/docs/source/research.bib
@@ -1,6 +1,6 @@
 %%% ARXIV TO BE UPDATED %%%
 @article{Giner2019Jul,
-        author = {Giner, Emmanuel and Scemama, Anthony and Toulouse, Julien and Loos, Pierre-Fran{\ifmmode\mbox{\c{c}}\else\c{c}\fi}ois},
+        author = {Giner, Emmanuel and Scemama, Anthony and Toulouse, Julien and Loos, Pierre-Fran{\c{c}}ois},
         title = {{Chemically Accurate Excitation Energies With Small Basis Sets}},
         journal = {arXiv},
         year = {2019},

From f4f75509dbb842b8c612641350afa6c13ba227f5 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Mon, 19 Aug 2019 20:16:33 +0200
Subject: [PATCH 19/21] Biblio (#58)

* Update biblio

* Update paper

* Journal missing in research.bib
---
 docs/source/research.bib | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/research.bib b/docs/source/research.bib
index f0c0648c..a2abea47 100644
--- a/docs/source/research.bib
+++ b/docs/source/research.bib
@@ -47,6 +47,7 @@
         pages = {084103},
         author = {Anthony Fert{\'{e}} and Emmanuel Giner and Julien Toulouse},
         title = {Range-separated multideterminant density-functional theory with a short-range correlation functional of the on-top pair density},
+        journal = {The Journal of Chemical Physics}
 }
 
 @article{Caffarel_2019,

From 8b14e190a9c9b9ea5218222334bcdc00a89db224 Mon Sep 17 00:00:00 2001
From: Thomas Applencourt <TApplencourt@users.noreply.github.com>
Date: Mon, 19 Aug 2019 17:13:41 -0500
Subject: [PATCH 20/21] Fix spurious EOF

---
 configure | 1 -
 1 file changed, 1 deletion(-)

diff --git a/configure b/configure
index 23f4aa02..6d875fae 100755
--- a/configure
+++ b/configure
@@ -330,7 +330,6 @@ EOF
 
                 opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
                 eval $(opam env)
-EOF
                 execute << EOF
                   opam install -y \${OCAML_PACKAGES}  || exit 1
 EOF

From 6148624fe799e304cecc9ca2805359314bede136 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 21 Aug 2019 16:29:23 +0200
Subject: [PATCH 21/21] Optimized qp_edit -n (#60)

---
 ocaml/Determinant.ml                |  4 ++--
 ocaml/Input_determinants_by_hand.ml | 18 +++++++++---------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/ocaml/Determinant.ml b/ocaml/Determinant.ml
index c27aefc4..6f248470 100644
--- a/ocaml/Determinant.ml
+++ b/ocaml/Determinant.ml
@@ -3,7 +3,8 @@ open Sexplib.Std
 
 type t = int64 array [@@deriving sexp]
 
-let to_int64_array (x:t) = (x:int64 array)
+external to_int64_array : t -> int64 array = "%identity"
+external of_int64_array_no_check : int64 array -> t = "%identity"
 
 
 let to_alpha_beta x =
@@ -61,7 +62,6 @@ let of_int64_array ~n_int ~alpha ~beta x =
      end;
    x
 
-let of_int64_array_no_check x = x
 
 let of_bitlist_couple ?n_int ~alpha ~beta (xa,xb) =
   let ba, bb =
diff --git a/ocaml/Input_determinants_by_hand.ml b/ocaml/Input_determinants_by_hand.ml
index e4c6ff2a..a676cf76 100644
--- a/ocaml/Input_determinants_by_hand.ml
+++ b/ocaml/Input_determinants_by_hand.ml
@@ -196,8 +196,9 @@ end = struct
 
   let write_psi_coef ~n_det ~n_states c =
     let n_det = Det_number.to_int n_det
-    and c = Array.to_list c
-            |> List.map Det_coef.to_float
+    and c =
+      Array.map Det_coef.to_float c
+      |> Array.to_list
     and n_states =
       States_number.to_int n_states
     in
@@ -239,12 +240,11 @@ end = struct
     assert (n_int = dim.(0));
     assert (dim.(1) = 2);
     assert (dim.(2) = (Det_number.to_int (read_n_det ())));
-    List.init dim.(2) (fun i ->
+    Array.init dim.(2) (fun i ->
       Array.sub data (2*n_int*i) (2*n_int) )
-    |> List.map (Determinant.of_int64_array
+    |> Array.map (Determinant.of_int64_array
       ~n_int:(N_int_number.of_int n_int)
       ~alpha:n_alpha ~beta:n_beta )
-    |> Array.of_list
   ;;
 
   let write_psi_det ~n_int ~n_det d =
@@ -363,7 +363,7 @@ Determinants ::
 "
      (b.expected_s2   |> Positive_float.to_string)
      (b.n_det         |> Det_number.to_string)
-     (b.state_average_weight |> Array.to_list |> List.map Positive_float.to_string |> String.concat "\t")
+     (b.state_average_weight |> Array.map Positive_float.to_string |> Array.to_list |> String.concat "\t")
      det_text
      |> Rst_string.of_string
   ;;
@@ -387,10 +387,10 @@ psi_det                = %s
      (b.n_states      |> States_number.to_string)
      (b.expected_s2   |> Positive_float.to_string)
      (b.state_average_weight |> Array.to_list |> List.map Positive_float.to_string |> String.concat ",")
-     (b.psi_coef  |> Array.to_list |> List.map Det_coef.to_string
+     (b.psi_coef  |> Array.map Det_coef.to_string |> Array.to_list
       |> String.concat ", ")
-     (b.psi_det   |> Array.to_list |> List.map (Determinant.to_string
-       ~mo_num) |> String.concat "\n\n")
+     (b.psi_det   |> Array.map (Determinant.to_string ~mo_num) |> Array.to_list
+      |> String.concat "\n\n")
   ;;
 
   let of_rst r =