Merge branch 'master' into dev

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.
 

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
 
 ```

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 
-                  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
-                  eval \$(\${QP_ROOT}/bin/opam env)
+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
+                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

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

@@ -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
@@ -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