Merge branch 'dev' into dev-lct

GITHUB.md

@@ -2,20 +2,23 @@ GitHub Branches
 ===============
 
 master:
-  The current up-to-date working branch, that users download It should
+  The current up-to-date working branch, that users download. It should
-  only contain the latest release and bug fixes.
+  only contain the latest stable release and bug fixes.
 
-develop-lcpq:
+dev:
-  Toulouse development branch  
-
-develop-lct:
-  Paris development branch  
-
-develop:
   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.
 

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 `${QP_ROOT}/bin/opam env`
+
+  If the installation fails because of bwrap, you can initialize opam using:
+
+  .. code:: bash
+
+      opam init --disable-sandboxing --comp=4.07.1
       eval `${QP_ROOT}/bin/opam env`
 
 * Install the required external OCaml libraries

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
 
 ```

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

configure

@@ -303,23 +303,31 @@ 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
+                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
+
             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
                 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
+                opam switch create ocaml-base-compiler.4.07.1     || exit 1
-                  eval \$(\${QP_ROOT}/bin/opam env)
+                opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
+                eval $(opam env)
+EOF
+                execute << EOF
                   opam install -y \${OCAML_PACKAGES}  || exit 1
 EOF
             fi

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}},

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_kinetic_integrals` which are the kinetic operator integrals on the |AO| basis 
-* `ao_nucl_elec_integral` which are the nuclear-elctron operator integrals on the |AO| basis (see :file:`pot_ao_ints.irp.f`)
+* `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 (see :file:`ao_mono_ints.irp.f`)
+* `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`.

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
 

src/cipsi/run_selection_slave.irp.f

@@ -73,7 +73,7 @@ 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.
@@ -84,6 +84,7 @@ 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
@@ -131,7 +132,6 @@ 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
 
-  if (b%cur > 0) then
 
   rc = f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)
   if(rc /= 8*N_states) then
@@ -148,6 +148,8 @@ subroutine push_selection_results(zmq_socket_push, pt2, variance, norm, b, task_
     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, 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)'
@@ -202,7 +204,10 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
     print *,  'f77_zmq_recv( zmq_socket_pull, N, 4, 0)'
   endif
 
-  if (N>0) then
+  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)'
@@ -218,6 +223,7 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
     print *,  'f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)'
   endif
 
+  if (N>0) then
       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)'
@@ -227,10 +233,6 @@ 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)

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)

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 ]

src/fci/pt2.irp.f

@@ -43,8 +43,13 @@ subroutine run
   E_CI_before(:) = psi_energy(:) + nuclear_repulsion
   relative_error=PT2_relative_error
 
+  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

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

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

src/utils/c_funcs.c

@@ -0,0 +1,6 @@
+#include <unistd.h>
+
+void usleep_c(int s)
+{
+  usleep((useconds_t) s);
+}

src/utils/c_functions.f90

@@ -0,0 +1,21 @@
+module c_functions
+  use iso_c_binding
+
+  interface
+    subroutine usleep_c(us) bind (C,name="usleep_c")
+      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
+  integer(c_int) :: u
+  u = us
+  call usleep_c(u)
+end

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

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
@@ -752,7 +751,8 @@ 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 +768,7 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task)
     add_task_to_taskserver = -1
     return
   endif
+  deallocate(message)
 
 end