From 590c5628e481cd1fc5f039d0b1caf31562abe545 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 28 Jul 2014 14:09:55 +0200 Subject: [PATCH] setup_environment.sh bug solved --- setup_environment.sh | 10 +-- src/CISD_SC2_selected/README.rst | 3 - src/Dets/README.rst | 8 +-- src/Full_CI/README.rst | 2 +- src/Hartree_Fock/README.rst | 110 ------------------------------- src/Output/README.rst | 15 ----- 6 files changed, 10 insertions(+), 138 deletions(-) diff --git a/setup_environment.sh b/setup_environment.sh index 76d82885..e79f07f8 100755 --- a/setup_environment.sh +++ b/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 PATH+=:\${QPACKAGE_ROOT}/scripts -export PATH+=:\${QPACKAGE_ROOT}/bin +export PYTHONPATH=\${PYTHONPATH}:\${QPACKAGE_ROOT}/scripts +export PATH=\${PATH}:\${QPACKAGE_ROOT}/scripts +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/ -source ${QPACKAGE_ROOT}/irpf90/bin/irpman +export PATH=\${PATH}:\${QPACKAGE_ROOT}/irpf90/bin/ +source \${QPACKAGE_ROOT}/irpf90/bin/irpman > /dev/null EOF source quantum_package.rc diff --git a/src/CISD_SC2_selected/README.rst b/src/CISD_SC2_selected/README.rst index b6206850..4c67caaa 100644 --- a/src/CISD_SC2_selected/README.rst +++ b/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 `_ - Undocumented - Needed Modules diff --git a/src/Dets/README.rst b/src/Dets/README.rst index b515ee76..a5707417 100644 --- a/src/Dets/README.rst +++ b/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 `_ +`copy_h_apply_buffer_to_wf `_ 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 `_ +`fill_h_apply_buffer_no_selection `_ Fill the H_apply buffer with determiants for CISD `h_apply_buffer_allocated `_ Buffer of determinants/coefficients/perturbative energy for H_apply. Uninitialized. Filled by H_apply subroutines. -`h_apply_threshold `_ +`h_apply_threshold `_ Theshold on | | -`resize_h_apply_buffer `_ +`resize_h_apply_buffer `_ Undocumented `cisd_sc2 `_ diff --git a/src/Full_CI/README.rst b/src/Full_CI/README.rst index dc2b86bf..ed9fa014 100644 --- a/src/Full_CI/README.rst +++ b/src/Full_CI/README.rst @@ -16,7 +16,7 @@ Documentation `n_det_max_fci `_ Max number od determinants in the wave function -`pt2_max `_ +`pt2_max `_ The selection process stops when the largest PT2 (for all the states) is lower than pt2_max in absolute value diff --git a/src/Hartree_Fock/README.rst b/src/Hartree_Fock/README.rst index 9fd7251e..0418aca5 100644 --- a/src/Hartree_Fock/README.rst +++ b/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 `_ - Alpha Fock matrix in AO basis set - -`ao_bi_elec_integral_beta `_ - Alpha Fock matrix in AO basis set - -`fock_matrix_alpha_ao `_ - Alpha Fock matrix in AO basis set - -`fock_matrix_alpha_mo `_ - Fock matrix on the MO basis - -`fock_matrix_ao `_ - Fock matrix in AO basis set - -`fock_matrix_beta_ao `_ - Alpha Fock matrix in AO basis set - -`fock_matrix_beta_mo `_ - Fock matrix on the MO basis - -`fock_matrix_diag_mo `_ - 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 `_ - 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 `_ - Undocumented - -`hf_energy `_ - Hartree-Fock energy - -`hf_density_matrix_ao `_ - Density matrix in the AO basis - -`hf_density_matrix_ao_alpha `_ - Alpha density matrix in the AO basis - -`hf_density_matrix_ao_beta `_ - Beta density matrix in the AO basis - -`run `_ - Undocumented - -`scf `_ - Undocumented - -`damping_scf `_ - Undocumented - -`diagonal_fock_matrix_mo `_ - Diagonal Fock matrix in the MO basis - -`diagonal_fock_matrix_mo_sum `_ - 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 `_ - Diagonal Fock matrix in the MO basis - -`do_diis `_ - If True, compute integrals on the fly - -`n_it_scf_max `_ - Maximum number of SCF iterations - -`thresh_scf `_ - Threshold on the convergence of the Hartree Fock energy - -`bi_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`kinetic_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`mono_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`nucl_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - -`ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - diff --git a/src/Output/README.rst b/src/Output/README.rst index 9e7c22cb..edbb7ff4 100644 --- a/src/Output/README.rst +++ b/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 `_ - Initial CPU and wall times when printing in the output files - -`output_wall_time_0 `_ - Initial CPU and wall times when printing in the output files - -`write_double `_ - Write a double precision value in output - -`write_int `_ - Write an integer value in output - -`write_time `_ - Write a time stamp in the output for chronological reconstruction -