setup_environment.sh bug solved

setup_environment.sh

@@ -20,12 +20,12 @@ fi
 cat << EOF > quantum_package.rc
 export IRPF90=${IRPF90}
 export QPACKAGE_ROOT=${QPACKAGE_ROOT}
-export PYTHONPATH+=:\${QPACKAGE_ROOT}/scripts
+export PYTHONPATH=\${PYTHONPATH}:\${QPACKAGE_ROOT}/scripts
-export PATH+=:\${QPACKAGE_ROOT}/scripts
+export PATH=\${PATH}:\${QPACKAGE_ROOT}/scripts
-export PATH+=:\${QPACKAGE_ROOT}/bin
+export PATH=\${PATH}:\${QPACKAGE_ROOT}/bin
 export QPACKAGE_CACHE_URL="http://qmcchem.ups-tlse.fr/files/scemama/quantum_package/cache"
-export PATH+=:${QPACKAGE_ROOT}/irpf90/bin/
+export PATH=\${PATH}:\${QPACKAGE_ROOT}/irpf90/bin/
-source ${QPACKAGE_ROOT}/irpf90/bin/irpman
+source \${QPACKAGE_ROOT}/irpf90/bin/irpman > /dev/null
 EOF
 
 source quantum_package.rc

src/CISD_SC2_selected/README.rst

@@ -8,9 +8,6 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/cisd_sc2_selection.irp.f#L1>`_
-  Undocumented
-
 
 
 Needed Modules

src/Dets/README.rst

@@ -50,21 +50,21 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L112>`_
+`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L113>`_
   Copies the H_apply buffer to psi_coef. You need to touch psi_det, psi_coef and N_det
   after calling this function.
 
-`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L198>`_
+`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L199>`_
   Fill the H_apply buffer with determiants for CISD
 
 `h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L14>`_
   Buffer of determinants/coefficients/perturbative energy for H_apply.
   Uninitialized. Filled by H_apply subroutines.
 
-`h_apply_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L44>`_
+`h_apply_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L45>`_
   Theshold on | <Di|H|Dj> |
 
-`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L62>`_
+`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L63>`_
   Undocumented
 
 `cisd_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L1>`_

src/Full_CI/README.rst

@@ -16,7 +16,7 @@ Documentation
 `n_det_max_fci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/parameters.irp.f#L1>`_
   Max number od determinants in the wave function
 
-`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/parameters.irp.f#L37>`_
+`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/parameters.irp.f#L36>`_
   The selection process stops when the largest PT2 (for all the states) is lower than pt2_max
   in absolute value
 

src/Hartree_Fock/README.rst

@@ -26,115 +26,5 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L102>`_
-  Alpha Fock matrix in AO basis set
-
-`ao_bi_elec_integral_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L103>`_
-  Alpha Fock matrix in AO basis set
-
-`fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_
-  Alpha Fock matrix in AO basis set
-
-`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L194>`_
-  Fock matrix on the MO basis
-
-`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L242>`_
-  Fock matrix in AO basis set
-
-`fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L84>`_
-  Alpha Fock matrix in AO basis set
-
-`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L214>`_
-  Fock matrix on the MO basis
-
-`fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L2>`_
-  Fock matrix on the MO basis.
-  For open shells, the ROHF Fock Matrix is
-  .br
-  |   F-K    |  F + K/2  |    F     |
-  |---------------------------------|
-  | F + K/2  |     F     |  F - K/2 |
-  |---------------------------------|
-  |    F     |  F - K/2  |  F + K   |
-  .br
-  F = 1/2 (Fa + Fb)
-  .br
-  K = Fb - Fa
-  .br
-
-`fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L1>`_
-  Fock matrix on the MO basis.
-  For open shells, the ROHF Fock Matrix is
-  .br
-  |   F-K    |  F + K/2  |    F     |
-  |---------------------------------|
-  | F + K/2  |     F     |  F - K/2 |
-  |---------------------------------|
-  |    F     |  F - K/2  |  F + K   |
-  .br
-  F = 1/2 (Fa + Fb)
-  .br
-  K = Fb - Fa
-  .br
-
-`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L285>`_
-  Undocumented
-
-`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L233>`_
-  Hartree-Fock energy
-
-`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
-  Density matrix in the AO basis
-
-`hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
-  Alpha density matrix in the AO basis
-
-`hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
-  Beta density matrix in the AO basis
-
-`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L7>`_
-  Undocumented
-
-`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
-  Undocumented
-
-`damping_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/damping_SCF.irp.f#L1>`_
-  Undocumented
-
-`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
-  Diagonal Fock matrix in the MO basis
-
-`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L57>`_
-  diagonal element of the fock matrix calculated as the sum over all the interactions
-  with all the electrons in the RHF determinant
-  diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
-
-`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
-  Diagonal Fock matrix in the MO basis
-
-`do_diis <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L39>`_
-  If True, compute integrals on the fly
-
-`n_it_scf_max <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L21>`_
-  Maximum number of SCF iterations
-
-`thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L1>`_
-  Threshold on the convergence of the Hartree Fock energy
-
-`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L5>`_
-  Energy of the reference bitmask used in Slater rules
-
-`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L3>`_
-  Energy of the reference bitmask used in Slater rules
-
-`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L2>`_
-  Energy of the reference bitmask used in Slater rules
-
-`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L4>`_
-  Energy of the reference bitmask used in Slater rules
-
-`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L1>`_
-  Energy of the reference bitmask used in Slater rules
-
 
 

src/Output/README.rst

@@ -39,20 +39,5 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L2>`_
-  Initial CPU and wall times when printing in the output files
-
-`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L1>`_
-  Initial CPU and wall times when printing in the output files
-
-`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L58>`_
-  Write a double precision value in output
-
-`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L73>`_
-  Write an integer value in output
-
-`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L42>`_
-  Write a time stamp in the output for chronological reconstruction
-