diff --git a/docs/source/_static/links.rst b/docs/source/_static/links.rst index f95e3e70..96393b79 100644 --- a/docs/source/_static/links.rst +++ b/docs/source/_static/links.rst @@ -12,7 +12,6 @@ .. _Irene: http://www-hpc.cea.fr/en/complexe/tgcc-Irene.htm .. _IRPF90: http://irpf90.ups-tlse.fr .. _LAPACK: http://www.netlib.org/lapack/ -.. _Molden: http://cheminf.cmbi.ru.nl/molden/ .. _NECI: https://github.com/ghb24/NECI_STABLE .. _Ninja: https://ninja-build.org/ .. _NWChem: http://www.nwchem-sw.org/ @@ -53,12 +52,15 @@ .. |CIPSI| replace:: :abbr:`CIPSI (Configuration Interaction using a Perturbative Selection)` .. |CI| replace:: :abbr:`CI (Configuration Interaction)` .. |CISD| replace:: :abbr:`CISD (Configuration Interaction with Single and Double Excitations)` +.. |CASSCF| replace:: |CAS| - |SCF| .. |CIS| replace:: :abbr:`CIS (Configuration Interaction with Single Excitations)` -.. |DFT| replace:: :abbr:`DFT (Density Functional Theory)` .. |DDCI| replace:: :abbr:`DDCI (Difference Dedicated Configuration Interaction)` +.. |DFT| replace:: :abbr:`DFT (Density Functional Theory)` .. |DIIS| replace:: :abbr:`DIIS (Direct Inversion of the Iterative Subspace)` +.. |FCIQMC| replace:: |FCI| - |QMC| .. |FCI| replace:: :abbr:`FCI (Full Configuration Interaction)` .. |HF| replace:: :abbr:`HF (Hartree-Fock)` +.. |KS-DFT| replace:: :abbr:`KS-DFT (Kohn-Sham Density Functional Theory)` .. |MO| replace:: :abbr:`MO (Molecular Orbital)` .. |MOs| replace:: :abbr:`MOs (Molecular Orbitals)` .. |MP2| replace:: :abbr:`MP2 (Moller-Plesset second order perturbative correction)` @@ -67,15 +69,13 @@ .. |MRPT| replace:: :abbr:`MRPT (Multi-Reference Perturbation Theory)` .. |PT2| replace:: :abbr:`PT2 (Second order perturbative correction)` .. |QMC| replace:: :abbr:`QMC (Quantum Monte Carlo)` +.. |ROHF| replace:: :abbr:`ROHF (Restricted Open-Shell Hartree-Fock)` +.. |RSDFT| replace:: :abbr:`RSDFT (Range Separated Density Functional Theory)` +.. |RSH| replace:: :abbr:`RSH (Range Separated Hybrids)` .. |rst| replace:: :abbr:`RST (ReStructured Text)` .. |SCF| replace:: :abbr:`SCF (Self Consistent Field)` -.. |RSH| replace:: :abbr:`RSH (Range Separated Hybrids)` -.. |RSDFT| replace:: :abbr:`RSDFT (Range Separated Density Functional Theory)` -.. |KS-DFT| replace:: :abbr:`KS-DFT (Kohn-Sham Density Functional Theory)` .. |sCI| replace:: :abbr:`sCI (Selected-CI)` .. |WFT| replace:: :abbr:`WFT (Wave Function Theory)` -.. |CASSCF| replace:: |CAS| - |SCF| -.. |FCIQMC| replace:: |FCI| - |QMC| .. |kalpha| replace:: :math:`|\alpha \rangle` .. |H| replace:: :math:`\hat H` diff --git a/docs/source/conf.py b/docs/source/conf.py index 939793cd..8d6a023e 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -171,7 +171,7 @@ for f in os.listdir("users_guide"): for f in os.listdir("programs"): name = f.split('.')[0] - if name not in []: + if name not in [""]: filename = os.path.join("programs",name) man_pages.append( (filename, name, qpdoc, [author], 1) ) diff --git a/docs/source/intro/selected_ci.rst b/docs/source/intro/selected_ci.rst index 443a678f..21062e62 100644 --- a/docs/source/intro/selected_ci.rst +++ b/docs/source/intro/selected_ci.rst @@ -55,8 +55,6 @@ Simple Algorithm .. |SetDI| replace:: `\{|D_I\rangle\}^{(n)}` .. |Psi_n| replace:: `|\Psi^{(n)}\rangle` -.. |H| replace:: `\hat H` -.. |kalpha| replace:: `|\alpha\rangle` .. |kalpha_star| replace:: `\{ |\alpha \rangle \}_\star ^{(n)}` .. |ealpha| replace:: `e_\alpha` .. |EPT| replace:: `E_\text{PT2}` diff --git a/docs/source/modules/ao_basis.rst b/docs/source/modules/ao_basis.rst index f61e99e8..240f31d1 100644 --- a/docs/source/modules/ao_basis.rst +++ b/docs/source/modules/ao_basis.rst @@ -23,9 +23,13 @@ The |AO| coefficients are normalized as: {\tilde c}_{ki} = \frac{c_{ki}}{ \int \left( (x-X_A)^a (y-Y_A)^b (z-Z_A)^c e^{-\gamma_{ki} |{\bf r} - {\bf R}_A|^2} \right)^2 dr} -Warning: `ao_coef` contains the |AO| coefficients given in input. These do not -include the normalization constant of the |AO|. The `ao_coef_normalized` provider includes -this normalization factor. + +.. warning:: + + `ao_coef` contains the |AO| coefficients given in input. These do not + include the normalization constant of the |AO|. The `ao_coef_normalized` + provider includes this normalization factor. + The |AOs| are also sorted by increasing exponent to accelerate the calculation of the two electron integrals. @@ -1076,7 +1080,7 @@ Subroutines / functions double precision function ao_value(i,r) - return the value of the ith ao at point r + Returns the value of the i-th ao at point $\textbf{r}$ Needs: @@ -1101,9 +1105,12 @@ Subroutines / functions subroutine give_all_aos_and_grad_and_lapl_at_r(r,aos_array,aos_grad_array,aos_lapl_array) - input : r(1) ==> r(1) = x, r(2) = y, r(3) = z - output : aos_array(i) = ao(i) evaluated at r - : aos_grad_array(1,i) = gradient X of the ao(i) evaluated at r + input : r(1) ==> r(1) = x, r(2) = y, r(3) = z + + output : + + * aos_array(i) = ao(i) evaluated at $\textbf{r}$ + * aos_grad_array(1,i) = $\nabla_x$ of the ao(i) evaluated at $\textbf{r}$ Needs: @@ -1138,9 +1145,13 @@ Subroutines / functions subroutine give_all_aos_and_grad_at_r(r,aos_array,aos_grad_array) - input : r(1) ==> r(1) = x, r(2) = y, r(3) = z - output : aos_array(i) = ao(i) evaluated at r - : aos_grad_array(1,i) = gradient X of the ao(i) evaluated at r + input : r(1) ==> r(1) = x, r(2) = y, r(3) = z + + output : + + * aos_array(i) = ao(i) evaluated at ro + * aos_grad_array(1,i) = gradient X of the ao(i) evaluated at $\textbf{r}$ + Needs: @@ -1175,8 +1186,9 @@ Subroutines / functions subroutine give_all_aos_at_r(r,aos_array) - input : r == r(1) = x and so on - aos_array(i) = aos(i) evaluated in r + input : r == r(1) = x and so on + + output : aos_array(i) = aos(i) evaluated in $\textbf{r}$ Needs: @@ -1211,7 +1223,7 @@ Subroutines / functions subroutine give_all_aos_at_r_old(r,aos_array) - gives the values of aos at a given point r + Gives the values of |AOs| at a given point $\textbf{r}$ Needs: @@ -1231,7 +1243,8 @@ Subroutines / functions double precision function primitive_value(i,j,r) - return the value of the jth primitive of ith ao at point r WITHOUT THE COEF + Returns the value of the j-th primitive of the i-th |AO| at point $\textbf{r} + **without the coefficient** Needs: diff --git a/docs/source/modules/ao_one_e_ints.rst b/docs/source/modules/ao_one_e_ints.rst index 53f5844c..ae8bda04 100644 --- a/docs/source/modules/ao_one_e_ints.rst +++ b/docs/source/modules/ao_one_e_ints.rst @@ -232,8 +232,10 @@ Providers Second derivative matrix elements in the |AO| basis. - :math:`{\tt ao\_deriv2\_x} = - \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle` + .. math:: + + {\tt ao\_deriv2\_x} = + \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle Needs: @@ -271,8 +273,10 @@ Providers Second derivative matrix elements in the |AO| basis. - :math:`{\tt ao\_deriv2\_x} = - \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle` + .. math:: + + {\tt ao\_deriv2\_x} = + \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle Needs: @@ -310,8 +314,10 @@ Providers Second derivative matrix elements in the |AO| basis. - :math:`{\tt ao\_deriv2\_x} = - \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle` + .. math:: + + {\tt ao\_deriv2\_x} = + \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle Needs: @@ -642,7 +648,8 @@ Providers Kinetic energy integrals in the |AO| basis. - :math:`\langle \chi_i |\hat{T}| \chi_j \rangle` + :math:`\langle \chi_i |\hat{T}| \chi_j \rangle` + Needs: @@ -1331,7 +1338,8 @@ Providers power_A,power_B,C_center,n_pt_in,d,n_pt_out,mu_in) - Returns the explicit polynomial in terms of the $t$ variable of the following polynomial: + Returns the explicit polynomial in terms of the $t$ variable of the + following polynomial: $I_{x1}(a_x, d_x,p,q) \times I_{x1}(a_y, d_y,p,q) \times I_{x1}(a_z, d_z,p,q)$. @@ -1355,7 +1363,8 @@ Providers power_A,power_B,C_center,n_pt_in,d,n_pt_out,mu_in,p,p_inv,p_inv_2,p_new,P_center) - Returns the explicit polynomial in terms of the $t$ variable of the following polynomial: + Returns the explicit polynomial in terms of the $t$ variable of the + following polynomial: $I_{x1}(a_x, d_x,p,q) \times I_{x1}(a_y, d_y,p,q) \times I_{x1}(a_z, d_z,p,q)$. @@ -1724,7 +1733,7 @@ Subroutines / functions Subroutine that returns all integrals over $r$ of type - $\frac{ \erf(\mu * |r-R_C|) }{ |r-R_C| }$ + $\frac{ \erf(\mu * | r - R_C | ) }{ | r - R_C | }$ Needs: @@ -1812,8 +1821,12 @@ Subroutines / functions Computes the following integral : - $\int dr (x-A_x)^a (x-B_x)^b \exp(-\alpha (x-A_x)^2 - \beta (x-B_x)^2 ) - \frac{\erf(\mu |r-R_C|)}{|r-R_c|}$. + + .. math:: + + \int dr (x-A_x)^a (x-B_x)^b \exp(-\alpha (x-A_x)^2 - \beta (x-B_x)^2 ) + \frac{\erf(\mu | r - R_C | )}{ | r - R_C | }$. + Calls: @@ -1834,7 +1847,7 @@ Subroutines / functions Computes the following integral : - $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) \frac{\erf(\mu |r-R_C|)}{|r-R_C|}$. + $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) \frac{\erf(\mu | r - R_C | )}{ | r - R_C | }$. Needs: diff --git a/docs/source/modules/ao_two_e_erf_ints.rst b/docs/source/modules/ao_two_e_erf_ints.rst index 4e35de17..7ee24a88 100644 --- a/docs/source/modules/ao_two_e_erf_ints.rst +++ b/docs/source/modules/ao_two_e_erf_ints.rst @@ -587,11 +587,13 @@ Subroutines / functions double precision function ERI_erf(alpha,beta,delta,gama,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z) - ATOMIC PRIMTIVE two-electron integral between the 4 primitives :: - primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2) - primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2) - primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2) - primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2) + Atomic primtive two-electron integral between the 4 primitives : + + * primitive 1 : $x_1^{a_x} y_1^{a_y} z_1^{a_z} \exp(-\alpha * r1^2)$ + * primitive 2 : $x_1^{b_x} y_1^{b_y} z_1^{b_z} \exp(- \beta * r1^2)$ + * primitive 3 : $x_2^{c_x} y_2^{c_y} z_2^{c_z} \exp(-\delta * r2^2)$ + * primitive 4 : $x_2^{d_x} y_2^{d_y} z_2^{d_z} \exp(-\gamma * r2^2)$ + Needs: @@ -776,9 +778,11 @@ Subroutines / functions subroutine integrale_new_erf(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt) - calculate the integral of the polynom :: - I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q) - between ( 0 ; 1) + Calculate the integral of the polynomial : + + $I_x1(a_x+b_x, c_x+d_x,p,q) \, I_x1(a_y+b_y, c_y+d_y,p,q) \, I_x1(a_z+b_z, c_z+d_z,p,q)$ + + between $( 0 ; 1)$ Needs: diff --git a/docs/source/modules/ao_two_e_ints.rst b/docs/source/modules/ao_two_e_ints.rst index 9121ed30..3c833a90 100644 --- a/docs/source/modules/ao_two_e_ints.rst +++ b/docs/source/modules/ao_two_e_ints.rst @@ -362,7 +362,7 @@ Providers recursive subroutine I_x1_pol_mult_a1(c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in) - recursive function involved in the two-electron integral + Recursive function involved in the two-electron integral Called by: @@ -392,7 +392,7 @@ Providers recursive subroutine I_x1_pol_mult_a2(c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in) - recursive function involved in the two-electron integral + Recursive function involved in the two-electron integral Called by: @@ -422,7 +422,7 @@ Providers recursive subroutine I_x1_pol_mult_recurs(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in) - recursive function involved in the two-electron integral + Recursive function involved in the two-electron integral Called by: @@ -487,7 +487,7 @@ Providers recursive subroutine I_x2_pol_mult(c,B_10,B_01,B_00,C_00,D_00,d,nd,dim) - recursive function involved in the two-electron integral + Recursive function involved in the two-electron integral Called by: @@ -1027,7 +1027,8 @@ Subroutines / functions subroutine that returns the explicit polynom in term of the "t" variable of the following polynomw : - I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q) + + $I_{x_1}(a_x,d_x,p,q) \, I_{x_1}(a_y,d_y,p,q) \ I_{x_1}(a_z,d_z,p,q)$ Called by: @@ -1055,7 +1056,7 @@ Subroutines / functions subroutine I_x1_pol_mult(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in) - recursive function involved in the two-electron integral + Recursive function involved in the two-electron integral Called by: @@ -1119,9 +1120,10 @@ Subroutines / functions subroutine integrale_new(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt) - calculate the integral of the polynom :: - I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q) - between ( 0 ; 1) + Calculates the integral of the polynomial : + + $I_{x_1}(a_x+b_x,c_x+d_x,p,q) \, I_{x_1}(a_y+b_y,c_y+d_y,p,q) \, I_{x_1}(a_z+b_z,c_z+d_z,p,q)$ + in $( 0 ; 1)$ Needs: @@ -1186,8 +1188,9 @@ Subroutines / functions Returns the upper boundary of the degree of the polynomial involved in the - bielctronic integral : - Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z) + two-electron integral : + + $I_x(a_x,b_x,c_x,d_x) \, I_y(a_y,b_y,c_y,d_y) \, I_z(a_z,b_z,c_z,d_z)$ .. c:function:: push_integrals: diff --git a/docs/source/modules/aux_quantities.rst b/docs/source/modules/aux_quantities.rst index 3ded29f8..e71dc325 100644 --- a/docs/source/modules/aux_quantities.rst +++ b/docs/source/modules/aux_quantities.rst @@ -10,21 +10,22 @@ aux_quantities This module contains some global variables (such as densities and energies) -which are stored in the EZFIO folder in a different place than determinants. +which are stored in the |EZFIO| directory in a different place than determinants. This is used in practice to store density matrices which can be obtained from -any methods, as long as they are stored in the same MO basis which is used for +any method, as long as they are stored in the same |MO| basis which is used for the calculations. In |RSDFT| calculations, this can be done to perform damping -on the density in order to speed up convergence. +on the density in order to speed up the convergence. The main providers of that module are: -* `data_one_e_dm_alpha_mo` and `data_one_e_dm_beta_mo` which are the - one-body alpha and beta densities which are necessary read from the EZFIO - folder. +* :c:data:`data_one_e_dm_alpha_mo` and :c:data:`data_one_e_dm_beta_mo` which + are the one-body alpha and beta densities which are necessary read from the + |EZFIO| directory. Thanks to these providers you can use any density matrix that does not -necessary corresponds to that of the current wave function. +necessarily corresponds to that of the current wave function. + diff --git a/docs/source/modules/cipsi.rst b/docs/source/modules/cipsi.rst index 3e0d1aef..7b5c82fd 100644 --- a/docs/source/modules/cipsi.rst +++ b/docs/source/modules/cipsi.rst @@ -49,7 +49,7 @@ By default, the program will stop when more than one million determinants have been selected, or when the |PT2| energy is below :math:`10^{-4}`. The variational and |PT2| energies of the iterations are stored in the -|EZFIO| database, in the :ref:`iterations` module. +|EZFIO| database, in the :ref:`module_iterations` module. @@ -180,55 +180,6 @@ Providers -.. c:function:: pt2_collector: - - - File : :file:`cipsi/pt2_stoch_routines.irp.f` - - .. code:: fortran - - subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error, & - variance, norm, b, N_) - - - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`pt2_j` - * :c:data:`pt2_stoch_istate` - * :c:data:`n_states` - * :c:data:`pt2_f` - * :c:data:`pt2_w` - * :c:data:`n_det_generators` - * :c:data:`pt2_n_teeth` - * :c:data:`pt2_u` - - Called by: - - .. hlist:: - :columns: 3 - - * :c:func:`zmq_pt2` - - Calls: - - .. hlist:: - :columns: 3 - - * :c:func:`add_to_selection_buffer` - * :c:func:`check_mem` - * :c:func:`create_selection_buffer` - * :c:func:`delete_selection_buffer` - * :c:func:`end_zmq_to_qp_run_socket` - * :c:func:`pull_pt2_results` - * :c:func:`sleep` - * :c:func:`sort_selection_buffer` - * :c:func:`wall_time` - - .. c:var:: pt2_cw @@ -311,7 +262,6 @@ Providers * :c:data:`n_core_orb` * :c:data:`n_det_generators` * :c:data:`n_det_selectors` - * :c:data:`n_states` * :c:data:`psi_det_sorted_gen` @@ -455,7 +405,6 @@ Providers * :c:data:`n_core_orb` * :c:data:`n_det_generators` * :c:data:`n_det_selectors` - * :c:data:`n_states` * :c:data:`psi_det_sorted_gen` @@ -1164,6 +1113,54 @@ Subroutines / functions * :c:func:`run_slave_cipsi` +.. c:function:: pt2_collector: + + + File : :file:`cipsi/pt2_stoch_routines.irp.f` + + .. code:: fortran + + subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error, variance, norm, b, N_) + + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`pt2_j` + * :c:data:`pt2_stoch_istate` + * :c:data:`n_states` + * :c:data:`pt2_f` + * :c:data:`pt2_w` + * :c:data:`n_det_generators` + * :c:data:`pt2_n_teeth` + * :c:data:`pt2_u` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`zmq_pt2` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`add_to_selection_buffer` + * :c:func:`check_mem` + * :c:func:`create_selection_buffer` + * :c:func:`delete_selection_buffer` + * :c:func:`end_zmq_to_qp_run_socket` + * :c:func:`pull_pt2_results` + * :c:func:`sleep` + * :c:func:`sort_selection_buffer` + * :c:func:`wall_time` + + .. c:function:: pt2_find_sample: @@ -1633,21 +1630,31 @@ Subroutines / functions .. hlist:: :columns: 3 + * :c:data:`pt2_stoch_istate` + * :c:data:`psi_det` + * :c:data:`zmq_state` * :c:data:`psi_coef` * :c:data:`mpi_rank` - * :c:data:`zmq_state` - * :c:data:`state_average_weight` * :c:data:`mpi_master` - * :c:data:`pt2_stoch_istate` - * :c:data:`n_states` * :c:data:`n_det` - * :c:data:`pt2_e0_denominator` - * :c:data:`n_det_selectors` - * :c:data:`n_det_generators` - * :c:data:`psi_det` - * :c:data:`n_states_diag` * :c:data:`zmq_context` + * :c:data:`n_det_selectors` + * :c:data:`psi_occ_pattern_hii` + * :c:data:`state_average_weight` + * :c:data:`mo_num` + * :c:data:`nthreads_pt2` + * :c:data:`elec_alpha_num` + * :c:data:`pt2_e0_denominator` + * :c:data:`qp_max_mem` + * :c:data:`n_states_diag` + * :c:data:`s2_eig` * :c:data:`threshold_generators` + * :c:data:`det_to_occ_pattern` + * :c:data:`n_states` + * :c:data:`pt2_f` + * :c:data:`n_det_generators` + * :c:data:`n_int` + * :c:data:`psi_det_hii` Called by: @@ -1661,9 +1668,11 @@ Subroutines / functions .. hlist:: :columns: 3 + * :c:func:`check_mem` * :c:func:`davidson_slave_tcp` * :c:func:`mpi_print` * :c:func:`omp_set_nested` + * :c:func:`resident_memory` * :c:func:`run_pt2_slave` * :c:func:`run_selection_slave` * :c:func:`sleep` @@ -1832,13 +1841,12 @@ Subroutines / functions * :c:data:`n_states` * :c:data:`n_det` * :c:data:`psi_bilinear_matrix_transp_values` - * :c:data:`elec_alpha_num` + * :c:data:`psi_bilinear_matrix_values` * :c:data:`n_det_selectors` * :c:data:`psi_bilinear_matrix_transp_values` * :c:data:`psi_bilinear_matrix_values` * :c:data:`n_int` * :c:data:`psi_det_generators` - * :c:data:`psi_bilinear_matrix_values` * :c:data:`psi_det_alpha_unique` * :c:data:`psi_det_sorted` * :c:data:`psi_det_sorted` @@ -1859,7 +1867,6 @@ Subroutines / functions * :c:func:`apply_hole` * :c:func:`bitstring_to_list_ab` - * :c:func:`check_mem` * :c:func:`fill_buffer_double` * :c:func:`get_excitation_degree_spin` * :c:func:`isort` @@ -2103,14 +2110,15 @@ Subroutines / functions * :c:data:`pt2_stoch_istate` * :c:data:`psi_selectors` * :c:data:`psi_bilinear_matrix_values` - * :c:data:`psi_det_alpha_unique` + * :c:data:`psi_occ_pattern_hii` * :c:data:`pt2_e0_denominator` * :c:data:`pt2_n_teeth` * :c:data:`psi_selectors_coef_transp` * :c:data:`n_det` + * :c:data:`mo_two_e_integrals_in_map` * :c:data:`s2_eig` * :c:data:`pt2_j` - * :c:data:`mo_two_e_integrals_in_map` + * :c:data:`psi_det_alpha_unique` * :c:data:`psi_bilinear_matrix_transp_values` * :c:data:`state_average_weight` * :c:data:`mo_num` @@ -2119,16 +2127,18 @@ Subroutines / functions * :c:data:`mo_one_e_integrals` * :c:data:`elec_alpha_num` * :c:data:`nproc` + * :c:data:`qp_max_mem` * :c:data:`psi_bilinear_matrix_columns_loc` * :c:data:`threshold_generators` * :c:data:`psi_det_beta_unique` - * :c:data:`qp_max_mem` + * :c:data:`det_to_occ_pattern` * :c:data:`psi_bilinear_matrix_transp_rows_loc` * :c:data:`n_states` * :c:data:`pt2_f` * :c:data:`n_det_generators` * :c:data:`psi_bilinear_matrix_transp_values` * :c:data:`n_int` + * :c:data:`psi_det_hii` * :c:data:`pt2_j` * :c:data:`psi_det_sorted` * :c:data:`pt2_w` diff --git a/docs/source/modules/cis.rst b/docs/source/modules/cis.rst index 10700afb..7943d7ce 100644 --- a/docs/source/modules/cis.rst +++ b/docs/source/modules/cis.rst @@ -8,34 +8,39 @@ cis === -This module contains a CIS program. +This module contains a |CIS| program. The user point of view ---------------------- -The :command:`cis` program performs the CI of the ROHF-like + all single excitations on top of it. -This program can be very useful to : +The :ref:`cis` program performs the CI to obtain the ROHF reference + all +single excitations on top of it. This program can be very useful to: -* **Ground state calculations**: generate a guess for the ground state wave function if one is not sure that the :c:func:`scf` program gave the lowest SCF solution. In combination with :c:func:`save_natorb` it can produce new |MOs| in order to reperform an :c:func:`scf` optimization. +* **Ground state calculations**: generate a guess for the ground state wave + function if one is not sure that the :ref:`scf` program gave the lowest |SCF| + solution. In combination with :ref:`save_natorb` it can produce new |MOs| in + order to reperform an :ref:`scf` optimization. -* **Excited states calculations**: generate guess for all the :option:`determinants n_states` wave functions, that will be used by the :c:func:`fci` program. +* **Excited states calculations**: generate guesses for all the + :option:`determinants n_states` wave functions, that will be used by the + :ref:`fci` program. The main keywords/options to be used are: -* :option:`determinants n_states` : number of states to consider for the |CIS| calculation +* :option:`determinants n_states`: number of states to consider for the |CIS| calculation -* :option:`determinants s2_eig` : force all states to have the desired value of :math:`S^2` +* :option:`determinants s2_eig`: force all states to have the desired value of |S^2| -* :option:`determinants expected_s2` : desired value of :math:`S^2` +* :option:`determinants expected_s2`: desired value of |S^2| -The programmer point of view ----------------------------- +The programmer's point of view +------------------------------ -This module have been built by setting the following rules: +This module was built by setting the following rules: * The only generator determinant is the Hartree-Fock (single-reference method) * All generated singly excited determinants are included in the wave function (no perturbative diff --git a/docs/source/modules/davidson.rst b/docs/source/modules/davidson.rst index b29d42ff..9a4eab1e 100644 --- a/docs/source/modules/davidson.rst +++ b/docs/source/modules/davidson.rst @@ -9,15 +9,22 @@ davidson ======== Abstract module for Davidson's diagonalization. -It contains everything required for the Davidson algorithm, dressed or not. If -a dressing is used, the dressing column should be defined and the -:ref:`davidson_dressed` module should be used. If no dressing is required, -the :ref:`davidson` module should be used, and it has a default zero dressing vector. +It contains everything required for the Davidson algorithm, dressed or +not. If a dressing is used, the dressing column should be defined and +the :ref:`module_davidson_dressed` module should be used. If no dressing +is required, the :ref:`module_davidson` module should be used, and it +has a default zero dressing vector. The important providers for that module are: -# `psi_energy` which is the expectation value over the wave function (`psi_det`, `psi_coef`) of the Hamiltonian, dressed or not. It uses the general subroutine `u_0_H_u_0`. -# `psi_energy_two_e` which is the expectation value over the wave function (`psi_det`, `psi_coef`) of the standard two-electrons coulomb operator. It uses the general routine `u_0_H_u_0_two_e`. +#. :c:data:`psi_energy` which is the expectation value over the wave + function (:c:data:`psi_det`, :c:data:`psi_coef`) of the Hamiltonian, + dressed or not. It uses the general subroutine :c:func:`u_0_H_u_0`. + +#. :c:data:`psi_energy_two_e` which is the expectation value over the + wave function (:c:data:`psi_det`, :c:data:`psi_coef`) of the standard + two-electron Coulomb operator. It uses the general routine + :c:func:`u_0_H_u_0_two_e`. @@ -40,7 +47,7 @@ EZFIO parameters Number of micro-iterations before re-contracting - Default: 8 + Default: 15 .. option:: state_following @@ -585,7 +592,6 @@ Subroutines / functions * :c:data:`psi_det_beta_unique` * :c:data:`only_expected_s2` * :c:data:`distributed_davidson` - * :c:data:`n_states` * :c:data:`n_int` Called by: @@ -626,7 +632,6 @@ Subroutines / functions .. hlist:: :columns: 3 - * :c:data:`n_states_diag` * :c:data:`nthreads_davidson` @@ -682,7 +687,6 @@ Subroutines / functions .. hlist:: :columns: 3 - * :c:data:`n_states_diag` * :c:data:`nthreads_davidson` @@ -696,7 +700,7 @@ Subroutines / functions subroutine davidson_pull_results(zmq_socket_pull, v_t, s_t, imin, imax, task_id) - Pull the results of $H|U \rangle$ on the master. + Pull the results of $H | U \rangle$ on the master. Needs: @@ -724,7 +728,7 @@ Subroutines / functions subroutine davidson_push_results(zmq_socket_push, v_t, s_t, imin, imax, task_id) - Push the results of $H|U \rangle$ from a worker to the master. + Push the results of $H | U \rangle$ from a worker to the master. Needs: @@ -850,6 +854,7 @@ Subroutines / functions :columns: 3 * :c:data:`psi_det_beta_unique` + * :c:data:`mpi_rank` * :c:data:`psi_bilinear_matrix_order_transp_reverse` * :c:data:`psi_det_alpha_unique` * :c:data:`mpi_initialized` @@ -858,6 +863,7 @@ Subroutines / functions * :c:data:`psi_bilinear_matrix_values` * :c:data:`nproc` * :c:data:`ref_bitmask_energy` + * :c:data:`n_states_diag` * :c:data:`psi_bilinear_matrix_columns_loc` Called by: @@ -874,7 +880,6 @@ Subroutines / functions * :c:func:`davidson_push_results` * :c:func:`h_s2_u_0_nstates_openmp_work` - * :c:func:`sleep` .. c:function:: diagonalize_ci: @@ -934,7 +939,7 @@ Subroutines / functions subroutine H_S2_u_0_nstates_openmp(v_0,s_0,u_0,N_st,sze) - Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$. + Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2 | u_0\rangle$. Assumes that the determinants are in psi_det @@ -977,7 +982,7 @@ Subroutines / functions subroutine H_S2_u_0_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t\rangle$ and $s_t = S^2 |u_t\rangle$ + Computes $v_t = H | u_t\rangle$ and $s_t = S^2 | u_t\rangle$ Default should be 1,N_det,0,1 @@ -1020,7 +1025,7 @@ Subroutines / functions subroutine H_S2_u_0_nstates_openmp_work_1(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$ Default should be 1,N_det,0,1 @@ -1072,7 +1077,7 @@ Subroutines / functions subroutine H_S2_u_0_nstates_openmp_work_2(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$ Default should be 1,N_det,0,1 @@ -1124,7 +1129,7 @@ Subroutines / functions subroutine H_S2_u_0_nstates_openmp_work_3(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$ Default should be 1,N_det,0,1 @@ -1176,7 +1181,7 @@ Subroutines / functions subroutine H_S2_u_0_nstates_openmp_work_4(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$ Default should be 1,N_det,0,1 @@ -1228,7 +1233,7 @@ Subroutines / functions subroutine H_S2_u_0_nstates_openmp_work_N_int(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t\rangle$ Default should be 1,N_det,0,1 @@ -1280,13 +1285,13 @@ Subroutines / functions subroutine H_S2_u_0_nstates_zmq(v_0,s_0,u_0,N_st,sze) - Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$ + Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2 | u_0\rangle$ n : number of determinants - H_jj : array of $\langle j|H|j \rangle$ + H_jj : array of $\langle j | H | j \rangle$ - S2_jj : array of $\langle j|S^2|j \rangle$ + S2_jj : array of $\langle j | S^2 | j \rangle$ Needs: @@ -1303,7 +1308,6 @@ Subroutines / functions * :c:data:`psi_bilinear_matrix_values` * :c:data:`nproc` * :c:data:`ref_bitmask_energy` - * :c:data:`n_states_diag` * :c:data:`psi_bilinear_matrix_columns_loc` Called by: @@ -1327,13 +1331,6 @@ Subroutines / functions * :c:func:`new_parallel_job` * :c:func:`omp_set_nested` - Touches: - - .. hlist:: - :columns: 3 - - * :c:data:`n_states_diag` - .. c:function:: h_s2_u_0_two_e_nstates_openmp: @@ -1345,7 +1342,7 @@ Subroutines / functions subroutine H_S2_u_0_two_e_nstates_openmp(v_0,s_0,u_0,N_st,sze) - Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$ + Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2 | u_0\rangle$ Assumes that the determinants are in psi_det @@ -1387,7 +1384,7 @@ Subroutines / functions subroutine H_S2_u_0_two_e_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t\rangle$ and $s_t = S^2 |u_t\rangle$ + Computes $v_t = H | u_t\rangle$ and $s_t = S^2 | u_t\rangle$ Default should be 1,N_det,0,1 @@ -1429,7 +1426,7 @@ Subroutines / functions subroutine H_S2_u_0_two_e_nstates_openmp_work_1(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t \rangle$ Default should be 1,N_det,0,1 @@ -1479,7 +1476,7 @@ Subroutines / functions subroutine H_S2_u_0_two_e_nstates_openmp_work_2(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t \rangle$ Default should be 1,N_det,0,1 @@ -1529,7 +1526,7 @@ Subroutines / functions subroutine H_S2_u_0_two_e_nstates_openmp_work_3(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t \rangle$ Default should be 1,N_det,0,1 @@ -1579,7 +1576,7 @@ Subroutines / functions subroutine H_S2_u_0_two_e_nstates_openmp_work_4(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t \rangle$ Default should be 1,N_det,0,1 @@ -1629,7 +1626,7 @@ Subroutines / functions subroutine H_S2_u_0_two_e_nstates_openmp_work_N_int(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep) - Computes $v_t = H|u_t angle$ and $s_t = S^2 |u_t angle$ + Computes $v_t = H | u_t \rangle$ and $s_t = S^2 | u_t \rangle$ Default should be 1,N_det,0,1 @@ -1679,9 +1676,9 @@ Subroutines / functions subroutine u_0_H_u_0(e_0,s_0,u_0,n,keys_tmp,Nint,N_st,sze) - Computes $E_0 = \frac{\langle u_0|H|u_0 \rangle}{\langle u_0|u_0 \rangle}$ + Computes $E_0 = \frac{\langle u_0 | H | u_0 \rangle}{\langle u_0 | u_0 \rangle}$ - and $S_0 = \frac{\langle u_0|S^2|u_0 \rangle}{\langle u_0|u_0 \rangle}$ + and $S_0 = \frac{\langle u_0 | S^2 | u_0 \rangle}{\langle u_0 | u_0 \rangle}$ n : number of determinants @@ -1692,7 +1689,6 @@ Subroutines / functions :columns: 3 * :c:data:`n_states_diag` - * :c:data:`n_states` * :c:data:`distributed_davidson` Called by: @@ -1710,13 +1706,6 @@ Subroutines / functions * :c:func:`h_s2_u_0_nstates_openmp` * :c:func:`h_s2_u_0_nstates_zmq` - Touches: - - .. hlist:: - :columns: 3 - - * :c:data:`n_states_diag` - .. c:function:: u_0_h_u_0_two_e: @@ -1728,7 +1717,7 @@ Subroutines / functions subroutine u_0_H_u_0_two_e(e_0,u_0,n,keys_tmp,Nint,N_st,sze) - Computes $E_0 = \frac{ \langle u_0|H|u_0\rangle}{\langle u_0|u_0 \rangle}$. + Computes $E_0 = \frac{ \langle u_0 | H | u_0\rangle}{\langle u_0 | u_0 \rangle}$. n : number of determinants diff --git a/docs/source/modules/density_for_dft.rst b/docs/source/modules/density_for_dft.rst index 28708f69..ad42369b 100644 --- a/docs/source/modules/density_for_dft.rst +++ b/docs/source/modules/density_for_dft.rst @@ -9,12 +9,16 @@ density_for_dft =============== -This module defines the *provider* of the density used for the DFT related calculations. -This definition is done through the keyword :option:`density_for_dft density_for_dft`. -The density can be: +This module defines the *provider* of the density used for the |DFT| related +calculations. This definition is done through the keyword +:option:`density_for_dft density_for_dft`. The density can be: -* WFT : the density is computed with a potentially multi determinant wave function (see variables `psi_det` and `psi_det`)# input_density : the density is set to a density previously stored in the |EZFIO| folder (see ``aux_quantities``) -* damping_rs_dft : the density is damped between the input_density and the WFT density, with a damping factor of :option:`density_for_dft damping_for_rs_dft` +* `WFT`: the density is computed with a potentially multi determinant wave + function (see variables `psi_det` and `psi_det`)# input_density: the density + is set to a density previously stored in the |EZFIO| directory (see + ``aux_quantities``) +* `damping_rs_dft`: the density is damped between the input_density and the WFT + density, with a damping factor of :option:`density_for_dft damping_for_rs_dft` diff --git a/docs/source/modules/determinants.rst b/docs/source/modules/determinants.rst index e6f1ddd7..f3636982 100644 --- a/docs/source/modules/determinants.rst +++ b/docs/source/modules/determinants.rst @@ -13,15 +13,15 @@ Contains everything for the computation of the Hamiltonian matrix elements in th The main providers for this module are: * :option:`determinants n_states`: number of states to be computed -* `psi_det`: list of determinants in the wave function used in many routines/providers of the |QP|. -* `psi_coef`: list of coefficients, for all :option:`determinants n_states` states, and all determinants. +* :c:data:`psi_det`: list of determinants in the wave function used in many routines/providers of the |QP|. +* :c:data:`psi_coef`: list of coefficients, for all :option:`determinants n_states` states, and all determinants. The main routines for this module are: -* `i_H_j`: computes the Hamiltonian matrix element between two arbitrary Slater determinants. -* `i_H_j_s2`: computes the Hamiltonian and (:math:`S^2`) matrix element between two arbitrary Slater determinants. -* `i_H_j_verbose`: returns the decomposition in terms of one- and two-body components of the Hamiltonian matrix elements between two arbitrary Slater determinants. Also return the fermionic phase factor. -* `i_H_psi`: computes the Hamiltonian matrix element between an arbitrary Slater determinant and a wave function composed of a sum of arbitrary Slater determinants. +* :c:func:`i_H_j`: computes the Hamiltonian matrix element between two arbitrary Slater determinants. +* :c:func:`i_H_j_s2`: computes the Hamiltonian and (|S^2|) matrix element between two arbitrary Slater determinants. +* :c:func:`i_H_j_verbose`: returns the decomposition in terms of one- and two-body components of the Hamiltonian matrix elements between two arbitrary Slater determinants. Also return the fermionic phase factor. +* :c:func:`i_H_psi`: computes the Hamiltonian matrix element between an arbitrary Slater determinant and a wave function composed of a sum of arbitrary Slater determinants. For an example of how to use these routines and providers, take a look at :file:`example.irp.f`. @@ -81,12 +81,12 @@ EZFIO parameters .. option:: n_int - Number of integers required to represent bitstrings (set in module :ref:`bitmask`) + Number of integers required to represent bitstrings (set in module :ref:`module_bitmask`) .. option:: bit_kind - (set in module :ref:`bitmask`) + (set in module :ref:`module_bitmask`) .. option:: mo_label diff --git a/docs/source/modules/dft_utils_in_r.rst b/docs/source/modules/dft_utils_in_r.rst index 4a011cc8..3e3fd5f1 100644 --- a/docs/source/modules/dft_utils_in_r.rst +++ b/docs/source/modules/dft_utils_in_r.rst @@ -769,13 +769,19 @@ Subroutines / functions subroutine density_and_grad_alpha_beta_and_all_aos_and_grad_aos_at_r(r,dm_a,dm_b, grad_dm_a, grad_dm_b, aos_array, grad_aos_array) - input : r(1) ==> r(1) = x, r(2) = y, r(3) = z - output : dm_a = alpha density evaluated at r - : dm_b = beta density evaluated at r - : aos_array(i) = ao(i) evaluated at r - : grad_dm_a(1) = X gradient of the alpha density evaluated in r - : grad_dm_a(1) = X gradient of the beta density evaluated in r - : grad_aos_array(1) = X gradient of the aos(i) evaluated at r + input: + + * r(1) ==> r(1) = x, r(2) = y, r(3) = z + + output: + + * dm_a = alpha density evaluated at r + * dm_b = beta density evaluated at r + * aos_array(i) = ao(i) evaluated at r + * grad_dm_a(1) = X gradient of the alpha density evaluated in r + * grad_dm_a(1) = X gradient of the beta density evaluated in r + * grad_aos_array(1) = X gradient of the aos(i) evaluated at r + Needs: diff --git a/docs/source/modules/fci.rst b/docs/source/modules/fci.rst index 2631511b..2d2bb639 100644 --- a/docs/source/modules/fci.rst +++ b/docs/source/modules/fci.rst @@ -15,43 +15,52 @@ fci The user point of view ---------------------- -* :c:func:`fci` performs |CIPSI| calculations using a stochastic scheme for both the selection and the |PT2| contribution, -* :c:func:`pt2` computes the |PT2| contribution using the wave function stored in the |EZFIO| - database. +* :ref:`fci` performs |CIPSI| calculations using a stochastic scheme for both + the selection and the |PT2| contribution, + +* :ref:`pt2` computes the |PT2| contribution using the wave function stored in + the |EZFIO| database. The main keywords/options for this module are: -* :option:`determinants n_det_max` : maximum number of Slater determinants in the CIPSI wave function. The :command:`fci` program will stop when the size of the CIPSI wave function will exceed :option:`determinants n_det_max`. +* :option:`determinants n_det_max` : maximum number of Slater determinants in + the |CIPSI| wave function. The :ref:`fci` program will stop when the size of + the |CIPSI| wave function will exceed :option:`determinants n_det_max`. -* :option:`perturbation pt2_max` : absolute value of the |PT2| to stop the CIPSI calculation. Once the |PT2| :math:`<` :option:`perturbation pt2_max`, the CIPSI calculation stops. +* :option:`perturbation pt2_max` : absolute value of the |PT2| to stop the + |CIPSI| calculation. Once the abs(|PT2|) :math:`<` :option:`perturbation pt2_max`, + the |CIPSI| calculation stops. -* :option:`determinants n_states` : number of states to consider in the CIPSI calculation. +* :option:`determinants n_states` : number of states to consider in the |CIPSI| + calculation. -* :option:`determinants read_wf` : if False, starts with a ROHF-like determinant, if True, starts with the current wave function(s) stored in the |EZFIO| folder. +* :option:`determinants read_wf` : if |false|, starts with a |ROHF|-like + determinant, if |true|, starts with the current wave function(s) stored in + the |EZFIO| directory. .. note:: - For a multi-state calculation, it is recommended to start with :c:func:`cis` or :c:func:`cisd` - wave functions as a guess. + For a multi-state calculation, it is recommended to start with :ref:`cis` + or :ref:`cisd` wave functions as a guess. -* :option:`determinants s2_eig` : if True, systematically add all the determinants needed to have a pure value of :math:`S^2`. Also, if True, it tracks only the states having the good :option:`determinants expected_s2`. +* :option:`determinants expected_s2` : expected value of |S^2| for the + desired spin multiplicity. -.. note:: - For a multi-state calculation, it is recommended to start with :c:func:`cis` or :c:func:`cisd` - wave functions as a guess. - -* :option:`determinants expected_s2` : expected value of :math:`S^2` for the desired spin multiplicity. +* :option:`determinants s2_eig` : if |true|, systematically add all the + determinants needed to have a pure value of |S^2|. Also, if |true|, it + tracks only the states having the good :option:`determinants expected_s2`. -The programmer point of view ----------------------------- -This module have been created with the :ref:`cipsi` module. +The programmer's point of view +------------------------------ + +This module was created with the :ref:`module_cipsi` module. .. seealso:: - The documentation of the :ref:`cipsi` module. + The documentation of the :ref:`module_cipsi` module. diff --git a/docs/source/modules/hartree_fock.rst b/docs/source/modules/hartree_fock.rst index 9f818166..f8aa5135 100644 --- a/docs/source/modules/hartree_fock.rst +++ b/docs/source/modules/hartree_fock.rst @@ -14,9 +14,9 @@ calculations (the spatial part of the |MOs| is common for alpha and beta spinorbitals). The Hartree-Fock algorithm is a |SCF| and therefore is based on the -:ref:`module_scf_utils`` module. +:ref:`module_scf_utils` module. -The Fock matrix is defined in :file:`hartree_fock fock_matrix_hf.irp.f`. +The Fock matrix is defined in :file:`fock_matrix_hf.irp.f`. diff --git a/docs/source/modules/mo_basis.rst b/docs/source/modules/mo_basis.rst index 2038ca3a..aae2e481 100644 --- a/docs/source/modules/mo_basis.rst +++ b/docs/source/modules/mo_basis.rst @@ -562,9 +562,9 @@ Subroutines / functions Rotates the j-th |MO| with the k-th |MO| to give two new |MOs| that are - * $+ = \frac{1}{\sqrt{2}} (|j\rangle + |k\rangle)$ + * $+ = \frac{1}{\sqrt{2}} ( | j\rangle + | k\rangle)$ - * $- = \frac{1}{\sqrt{2}} (|j\rangle - |k\rangle)$ + * $- = \frac{1}{\sqrt{2}} ( | j\rangle - | k\rangle)$ by convention, the '+' |MO| is in the lowest index (min(j,k)) by convention, the '-' |MO| is in the highest index (max(j,k)) diff --git a/docs/source/modules/perturbation.rst b/docs/source/modules/perturbation.rst index fb144639..b933ca57 100644 --- a/docs/source/modules/perturbation.rst +++ b/docs/source/modules/perturbation.rst @@ -106,39 +106,6 @@ EZFIO parameters Providers --------- -.. c:function:: fill_h_apply_buffer_selection: - - - File : :file:`perturbation/selection.irp.f` - - .. code:: fortran - - subroutine fill_H_apply_buffer_selection(n_selected,det_buffer,e_2_pert_buffer,coef_pert_buffer, & - N_st,Nint,iproc,select_max_out) - - - Fill the H_apply buffer with determiants for the selection - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`selection_criterion` - * :c:data:`h_apply_buffer_allocated` - * :c:data:`n_det` - * :c:data:`n_int` - - Calls: - - .. hlist:: - :columns: 3 - - * :c:func:`omp_set_lock` - * :c:func:`omp_unset_lock` - * :c:func:`resize_h_apply_buffer` - - .. c:var:: h0_type @@ -253,6 +220,38 @@ Providers Subroutines / functions ----------------------- +.. c:function:: fill_h_apply_buffer_selection: + + + File : :file:`perturbation/selection.irp.f` + + .. code:: fortran + + subroutine fill_H_apply_buffer_selection(n_selected,det_buffer,e_2_pert_buffer,coef_pert_buffer, N_st,Nint,iproc,select_max_out) + + + Fill the H_apply buffer with determiants for the selection + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`selection_criterion` + * :c:data:`h_apply_buffer_allocated` + * :c:data:`n_det` + * :c:data:`n_int` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`omp_set_lock` + * :c:func:`omp_unset_lock` + * :c:func:`resize_h_apply_buffer` + + .. c:function:: perturb_buffer_by_mono_dummy: @@ -263,7 +262,7 @@ Subroutines / functions subroutine perturb_buffer_by_mono_dummy(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``dummy`` to the buffer of determinants generated in the H_apply + Apply pertubration ``dummy`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -298,7 +297,7 @@ Subroutines / functions subroutine perturb_buffer_by_mono_epstein_nesbet(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply + Apply pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -333,7 +332,7 @@ Subroutines / functions subroutine perturb_buffer_by_mono_epstein_nesbet_2x2(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply + Apply pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -368,7 +367,7 @@ Subroutines / functions subroutine perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply + Apply pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -403,7 +402,7 @@ Subroutines / functions subroutine perturb_buffer_by_mono_moller_plesset(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply + Apply pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -438,7 +437,7 @@ Subroutines / functions subroutine perturb_buffer_by_mono_qdpt(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``qdpt`` to the buffer of determinants generated in the H_apply + Apply pertubration ``qdpt`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -473,7 +472,7 @@ Subroutines / functions subroutine perturb_buffer_dummy(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``dummy`` to the buffer of determinants generated in the H_apply + Apply pertubration ``dummy`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -509,7 +508,7 @@ Subroutines / functions subroutine perturb_buffer_epstein_nesbet(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply + Apply pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -545,7 +544,7 @@ Subroutines / functions subroutine perturb_buffer_epstein_nesbet_2x2(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply + Apply pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -581,7 +580,7 @@ Subroutines / functions subroutine perturb_buffer_epstein_nesbet_2x2_no_ci_diag(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply + Apply pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -617,7 +616,7 @@ Subroutines / functions subroutine perturb_buffer_moller_plesset(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply + Apply pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply routine. Needs: @@ -653,7 +652,7 @@ Subroutines / functions subroutine perturb_buffer_qdpt(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) - Applly pertubration ``qdpt`` to the buffer of determinants generated in the H_apply + Apply pertubration ``qdpt`` to the buffer of determinants generated in the H_apply routine. Needs: diff --git a/docs/source/modules/scf_utils.rst b/docs/source/modules/scf_utils.rst index 5b06d6d0..3ab72f78 100644 --- a/docs/source/modules/scf_utils.rst +++ b/docs/source/modules/scf_utils.rst @@ -192,11 +192,11 @@ Providers .. code:: fortran - subroutine extrapolate_Fock_matrix( & - error_matrix_DIIS,Fock_matrix_DIIS, & - Fock_matrix_AO_,size_Fock_matrix_AO, & - iteration_SCF,dim_DIIS & -) + subroutine extrapolate_Fock_matrix( & + error_matrix_DIIS,Fock_matrix_DIIS, & + Fock_matrix_AO_,size_Fock_matrix_AO, & + iteration_SCF,dim_DIIS & + ) Compute the extrapolated Fock matrix using the DIIS procedure diff --git a/docs/source/modules/selectors_cassd.rst b/docs/source/modules/selectors_cassd.rst index 57704d5c..0740d91e 100644 --- a/docs/source/modules/selectors_cassd.rst +++ b/docs/source/modules/selectors_cassd.rst @@ -9,5 +9,5 @@ selectors_cassd =============== Selectors for |CAS-SD| calculations. The selectors are defined as first the -generators from :ref:`Generators_CAS`, and then the rest of the wave function. +generators from :ref:`module_generators_cas`, and then the rest of the wave function. diff --git a/docs/source/modules/utils.rst b/docs/source/modules/utils.rst index d2c76ba2..775cfc0d 100644 --- a/docs/source/modules/utils.rst +++ b/docs/source/modules/utils.rst @@ -855,8 +855,8 @@ Subroutines / functions * :c:func:`remove_duplicates_in_selection_buffer` * :c:func:`run_cipsi` * :c:func:`run_pt2_slave` + * :c:func:`run_slave_main` * :c:func:`run_stochastic_cipsi` - * :c:func:`select_singles_and_doubles` * :c:func:`selection_collector` * :c:func:`sort_selection_buffer` * :c:func:`testteethbuilding` @@ -2651,6 +2651,7 @@ Subroutines / functions * :c:func:`check_mem` * :c:func:`davidson_diag_hjj_sjj` * :c:func:`print_memory_usage` + * :c:func:`run_slave_main` * :c:func:`zmq_pt2` Calls: diff --git a/docs/source/programmers_guide/conventions.rst b/docs/source/programmers_guide/conventions.rst index ecd6d6b0..33fd810a 100644 --- a/docs/source/programmers_guide/conventions.rst +++ b/docs/source/programmers_guide/conventions.rst @@ -107,7 +107,7 @@ Only standard Fortran is allowed : Intel or GNU extensions are forbidden. The name of a program should be the same as the name of the file. For example, for the :ref:`fci` program, we have -.. code-block:: fortan +.. code-block:: fortran program fci diff --git a/docs/source/programmers_guide/ezfio.rst b/docs/source/programmers_guide/ezfio.rst index e96883bb..1eece851 100644 --- a/docs/source/programmers_guide/ezfio.rst +++ b/docs/source/programmers_guide/ezfio.rst @@ -8,7 +8,7 @@ EZFIO.cfg The simplest way to add control parameters in the |EZFIO| directory is to create a :file:`EZFIO.cfg` file in the module. An example can be found in existing modules -such as :ref:`hartree_fock`:: +such as :ref:`module_hartree_fock`:: [max_dim_diis] type: integer @@ -92,7 +92,7 @@ Optional It is possible to directly add to the current module |EZFIO| configuration files, named with the ``.ezfio_config`` suffix. An example is in the -:ref:`bitmask` module. +:ref:`module_bitmask` module. .. code:: text diff --git a/docs/source/programmers_guide/index_providers.rst b/docs/source/programmers_guide/index_providers.rst index 1b296fff..c9d65302 100644 --- a/docs/source/programmers_guide/index_providers.rst +++ b/docs/source/programmers_guide/index_providers.rst @@ -226,7 +226,6 @@ Index of Providers * :c:data:`ezfio_work_dir` * :c:data:`fact_inv` * :c:data:`file_lock` -* :c:data:`fill_h_apply_buffer_selection` * :c:data:`final_grid_points` * :c:data:`final_weight_at_r` * :c:data:`final_weight_at_r_vector` @@ -606,7 +605,6 @@ Index of Providers * :c:data:`psi_selectors_coef_transp` * :c:data:`psi_selectors_diag_h_mat` * :c:data:`psi_selectors_size` -* :c:data:`pt2_collector` * :c:data:`pt2_cw` * :c:data:`pt2_e0_denominator` * :c:data:`pt2_f` @@ -907,6 +905,7 @@ Index of Subroutines/Functions * :c:func:`fcidump` * :c:func:`fill_buffer_double` * :c:func:`fill_h_apply_buffer_no_selection` +* :c:func:`fill_h_apply_buffer_selection` * :c:func:`filter_connected` * :c:func:`filter_connected_i_h_psi0` * :c:func:`filter_not_connected` @@ -1198,6 +1197,7 @@ Index of Subroutines/Functions * :c:func:`provide_all_mo_integrals_erf` * :c:func:`provide_everything` * :c:func:`pt2` +* :c:func:`pt2_collector` * :c:func:`pt2_dummy` * :c:func:`pt2_epstein_nesbet` * :c:func:`pt2_epstein_nesbet_2x2` diff --git a/docs/source/programs/cis.rst b/docs/source/programs/cis.rst index ffbadf5f..4f496254 100644 --- a/docs/source/programs/cis.rst +++ b/docs/source/programs/cis.rst @@ -20,25 +20,22 @@ cis This program can be useful in many cases: - Ground state calculation - ------------------------ + 1. Ground state calculation - To be sure to have the lowest |SCF| solution, perform an :ref:`scf` - (see the :ref:`hartree_fock` module), then a :ref:`cis`, save - the natural orbitals (see :ref:`save_natorb`) and re-run an - :ref:`scf` optimization from this |MO| guess. + To be sure to have the lowest |SCF| solution, perform an :ref:`scf` + (see the :ref:`module_hartree_fock` module), then a :ref:`cis`, save the + natural orbitals (see :ref:`save_natorb`) and re-run an :ref:`scf` + optimization from this |MO| guess. - Excited states calculations - --------------------------- + 2. Excited states calculations - The lowest excited states are much likely to be dominated by - single-excitations. Therefore, running a :ref:`cis` will save - the `n_states` lowest states within the |CIS| space in the |EZFIO| - directory, which can afterwards be used as guess wave functions for - a further multi-state |FCI| calculation if :option:`determinants read_wf` - is set to |true| before running the :ref:`fci` - executable. + The lowest excited states are much likely to be dominated by + single-excitations. Therefore, running a :ref:`cis` will save the + `n_states` lowest states within the |CIS| space in the |EZFIO| + directory, which can afterwards be used as guess wave functions for + a further multi-state |FCI| calculation if :option:`determinants + read_wf` is set to |true| before running the :ref:`fci` executable. If :option:`determinants s2_eig` is set to |true|, the |CIS| diff --git a/docs/source/programs/cisd.rst b/docs/source/programs/cisd.rst index 8208dd06..8d3f5ab4 100644 --- a/docs/source/programs/cisd.rst +++ b/docs/source/programs/cisd.rst @@ -19,7 +19,7 @@ cisd This program can be useful in many cases: - * GROUND STATE CALCULATION: if even after a :c:func:`cis` calculation, natural + * **Ground state calculation**: if even after a :c:func:`cis` calculation, natural orbitals (see :c:func:`save_natorb`) and then :c:func:`scf` optimization, you are not sure to have the lowest scf solution, do the same strategy with the :c:func:`cisd` executable instead of the :c:func:`cis` exectuable to generate the natural @@ -27,11 +27,11 @@ cisd - * EXCITED STATES CALCULATIONS: the lowest excited states are much likely to + * **Excited states calculations**: the lowest excited states are much likely to be dominanted by single- or double-excitations. Therefore, running a :c:func:`cisd` will save the "n_states" lowest states within the CISD space - in the EZFIO folder, which can afterward be used as guess wave functions + in the |EZFIO| directory, which can afterward be used as guess wave functions for a further multi-state fci calculation if you specify "read_wf" = True before running the fci executable (see :option:`determinants read_wf`). Also, if you specify "s2_eig" = True, the cisd will only retain states @@ -50,6 +50,7 @@ cisd * "act" orbitals where an electron can be either excited from or to * "del" orbitals which will be never occupied + Needs: diff --git a/docs/source/programs/diagonalize_h.rst b/docs/source/programs/diagonalize_h.rst index e21da7c0..cd1f9e7b 100644 --- a/docs/source/programs/diagonalize_h.rst +++ b/docs/source/programs/diagonalize_h.rst @@ -9,11 +9,14 @@ diagonalize_h - Program that extracts the :option:`determinants n_states` lowest states of the Hamiltonian within the set of Slater determinants stored in the EZFIO folder. + Program that extracts the :option:`determinants n_states` lowest + states of the Hamiltonian within the set of Slater determinants stored + in the |EZFIO| directory. - If :option:`determinants s2_eig` = True, it will retain only states + If :option:`determinants s2_eig` = |true|, it will retain only states + which correspond to the desired value of + :option:`determinants expected_s2`. - which corresponds to the desired value of :option:`determinants expected_s2`. Needs: diff --git a/docs/source/programs/fci.rst b/docs/source/programs/fci.rst index f4b8b268..5ebd7da9 100644 --- a/docs/source/programs/fci.rst +++ b/docs/source/programs/fci.rst @@ -21,7 +21,7 @@ fci conditions: * number of Slater determinants > :option:`determinants n_det_max` - * |PT2| < :option:`perturbation pt2_max` + * abs(|PT2|) less than :option:`perturbation pt2_max` The following other options can be of interest: @@ -38,7 +38,7 @@ fci :option:`determinants expected_s2`. For excited states calculations, it is recommended to start with - :ref:`.cis.` or :ref:`.cisd.` guess wave functions, eventually in + :ref:`cis` or :ref:`cisd` guess wave functions, eventually in a restricted set of |MOs|, and to set :option:`determinants s2_eig` to |true|. diff --git a/docs/source/programs/fcidump.rst b/docs/source/programs/fcidump.rst index b6e2a5b4..4e58a1ff 100644 --- a/docs/source/programs/fcidump.rst +++ b/docs/source/programs/fcidump.rst @@ -9,17 +9,22 @@ fcidump - Produce a regular FCIDUMP file from the |MOs| stored in the |EZFIO| folder. + Produce a regular `FCIDUMP` file from the |MOs| stored in the |EZFIO| + directory. - To specify an active space, the class of the mos have to set in the |EZFIO| folder (see :ref:`qp_set_mo_class`). + To specify an active space, the class of the |MOs| have to set in the + |EZFIO| directory (see :ref:`qp_set_mo_class`). - The fcidump program supports 3 types of MO_class : + The :ref:`fcidump` program supports 3 types of |MO| classes : - * the "core" orbitals which are always doubly occupied in the calculation + * the *core* orbitals which are always doubly occupied in the + calculation - * the "del" orbitals that are never occupied in the calculation + * the *deleted* orbitals that are never occupied in the calculation + + * the *active* orbitals that are occupied with a varying number of + electrons - * the "act" orbitals that will be occupied by a varying number of electrons Needs: diff --git a/docs/source/programs/four_idx_transform.rst b/docs/source/programs/four_idx_transform.rst index 953d7b1d..220433e1 100644 --- a/docs/source/programs/four_idx_transform.rst +++ b/docs/source/programs/four_idx_transform.rst @@ -9,11 +9,15 @@ four_idx_transform - 4-index transformation of two-electron integrals from |AO| to |MO| integrals. + 4-index transformation of two-electron integrals from |AO| to |MO| + integrals. - This program will compute the two-electron integrals on the |MO| basis and store it into the |EZFIO| folder. + This program will compute the two-electron integrals on the |MO| basis + and store it into the |EZFIO| directory. + + This program can be useful if the AO --> MO transformation is an + expensive step by itself. - This program can be useful if the AO --> MO transformation is an expensive step by itself. Needs: diff --git a/docs/source/programs/molden.rst b/docs/source/programs/molden.rst index 23830392..9611bac0 100644 --- a/docs/source/programs/molden.rst +++ b/docs/source/programs/molden.rst @@ -9,7 +9,7 @@ molden - Produce a Molden file + Produces a Molden file Needs: diff --git a/docs/source/programs/print_wf.rst b/docs/source/programs/print_wf.rst index 56f5b238..a141be09 100644 --- a/docs/source/programs/print_wf.rst +++ b/docs/source/programs/print_wf.rst @@ -9,13 +9,15 @@ print_wf - Print the ground state wave function stored in the |EZFIO| folder in the intermediate normalization. + Print the ground state wave function stored in the |EZFIO| directory + in the intermediate normalization. - It also prints a lot of information regarding the excitation operators from the reference determinant + It also prints a lot of information regarding the excitation + operators from the reference determinant ! and a first-order + perturbative analysis of the wave function. - and a first-order perturbative analysis of the wave function. - - If the wave function strongly deviates from the first-order analysis, something funny is going on :) + If the wave function strongly deviates from the first-order analysis, + something funny is going on :) Needs: diff --git a/docs/source/programs/pt2.rst b/docs/source/programs/pt2.rst index c18e466b..45726526 100644 --- a/docs/source/programs/pt2.rst +++ b/docs/source/programs/pt2.rst @@ -9,13 +9,18 @@ pt2 - Second order perturbative correction to the wave function contained in the EZFIO directory. + Second order perturbative correction to the wave function contained + in the |EZFIO| directory. - This programs runs the stochastic PT2 correction on all "n_states" wave function stored in the EZFIO folder (see :option:`determinant n_states`). + This programs runs the stochastic |PT2| correction on all + :option:`determinants n_states` wave functions stored in the |EZFIO| + directory. - The option for the PT2 correction are the "pt2_relative_error" which is the relative stochastic + The main option for the |PT2| correction is the + :option:`perturbation pt2_relative_error` which is the relative + stochastic error on the |PT2| to reach before stopping the + sampling. - error on the PT2 to reach before stopping the stochastic sampling. (see :option:`perturbation pt2_relative_error`) Needs: diff --git a/docs/source/programs/save_natorb.rst b/docs/source/programs/save_natorb.rst index 736e4178..852b1583 100644 --- a/docs/source/programs/save_natorb.rst +++ b/docs/source/programs/save_natorb.rst @@ -9,15 +9,16 @@ save_natorb - Save natural MOs into the EZFIO + Save natural |MOs| into the |EZFIO|. - This program reads the wave function stored in the EZFIO folder, + This program reads the wave function stored in the |EZFIO| directory, + extracts the corresponding natural orbitals and setd them as the new + |MOs|. - extracts the corresponding natural orbitals and set them as the new MOs - - If this is a multi-state calculation, the density matrix that produces the natural orbitals - - is obtained from a state-averaged of the density matrices of each state with the corresponding state_average_weight (see the doc of state_average_weight). + If this is a multi-state calculation, the density matrix that produces + the natural orbitals is obtained from an average of the density + matrices of each state with the corresponding + :option:`determinants state_average_weight` Needs: diff --git a/docs/source/programs/save_one_e_dm.rst b/docs/source/programs/save_one_e_dm.rst index bf8ec089..5758aad6 100644 --- a/docs/source/programs/save_one_e_dm.rst +++ b/docs/source/programs/save_one_e_dm.rst @@ -9,12 +9,16 @@ save_one_e_dm - programs that computes the one body density on the mo basis for alpha and beta electrons - from the wave function stored in the EZFIO folder, and then save it into the EZFIO folder aux_quantities. + Program that computes the one body density on the |MO| basis + for $\alpha$ and $\beta$ electrons from the wave function + stored in the |EZFIO| directory, and then saves it into the + :ref:`module_aux_quantities`. - Then, the global variable data_one_e_dm_alpha_mo and data_one_e_dm_beta_mo will automatically read this density in a further calculation. - - This can be used to perform damping on the density in RS-DFT calculation (see the density_for_dft module). + Then, the global variable :option:`aux_quantities data_one_e_dm_alpha_mo` + and :option:`aux_quantities data_one_e_dm_beta_mo` will automatically + read this density in the next calculation. This can be used to perform + damping on the density in |RSDFT| calculations (see + :ref:`module_density_for_dft`). Needs: diff --git a/docs/source/programs/write_integrals_erf.rst b/docs/source/programs/write_integrals_erf.rst index b940e8b4..43cf853d 100644 --- a/docs/source/programs/write_integrals_erf.rst +++ b/docs/source/programs/write_integrals_erf.rst @@ -9,7 +9,8 @@ write_integrals_erf - Saves the two-electron integrals with the :math:`erf(\mu r_{12})/r_{12}` oprerator into the EZFIO folder + Saves the two-electron integrals with the $erf(\mu r_{12})/r_{12}$ + oprerator into the EZFIO directory. Needs: diff --git a/docs/source/users_guide/interfaces.rst b/docs/source/users_guide/interfaces.rst index c00b165e..dc443346 100644 --- a/docs/source/users_guide/interfaces.rst +++ b/docs/source/users_guide/interfaces.rst @@ -15,7 +15,7 @@ A few interfaces to external codes are available. |qp| -> \* ---------- -`Molden`_ +`Molden `_ 3D plots of Molecular Orbitals FCIDUMP diff --git a/docs/source/users_guide/printing.rst b/docs/source/users_guide/printing.rst index 8509a2d8..69f2b839 100644 --- a/docs/source/users_guide/printing.rst +++ b/docs/source/users_guide/printing.rst @@ -31,7 +31,7 @@ interactively in :ref:`qp_edit` mode. An alternative is to use the This program will, by default, print out the first :math:`10^4` determinants whatever the size of the wave function stored in the -|EZFIO| folder. If you want to change the number of printed Slater +|EZFIO| directory. If you want to change the number of printed Slater determinants, just change the :option:`determinants n_det_print_wf` keyword using the :ref:`qp_edit` tool. diff --git a/docs/source/users_guide/qp_reset.rst b/docs/source/users_guide/qp_reset.rst new file mode 100644 index 00000000..c92f2791 --- /dev/null +++ b/docs/source/users_guide/qp_reset.rst @@ -0,0 +1,32 @@ +.. _qp_reset: + +======== +qp_reset +======== + +.. program:: qp_reset + +This command resets parts of the |EZFIO| directory. + + +Usage +----- + +.. code:: bash + + qp_reset [-adhm] EZFIO_DIR + +.. option:: -a, --all + + Reset to the state in which the directory is after after running :ref:`qp_create_ezfio`. + +.. option:: -d, --dets + + Deletes the determinants and CI coefficients. + +.. option:: -m, --mos + + Deletes the |MOs|, and consequently the determinants and CI coefficients. + + + diff --git a/docs/source/users_guide/qpsh.rst b/docs/source/users_guide/qpsh.rst index 4cf1a612..7a1a874c 100644 --- a/docs/source/users_guide/qpsh.rst +++ b/docs/source/users_guide/qpsh.rst @@ -95,7 +95,7 @@ Running programs qp (run|srun|mpirun) [options] - Runs :ref:`qp_run`, :ref:`qp_srun`, or :ref:`qp_mpirun` using the current + Runs :ref:`qp_run`, :command:`qp_srun`, or :command:`qp_mpirun` using the current |EZFIO| directory. .. option:: stop diff --git a/docs/source/users_guide/quickstart.rst b/docs/source/users_guide/quickstart.rst index 2c04cbcb..d2de32c9 100644 --- a/docs/source/users_guide/quickstart.rst +++ b/docs/source/users_guide/quickstart.rst @@ -74,7 +74,8 @@ The expected energy is ``-92.827856698`` au. .. seealso:: - The documentation of the :ref:`hartree_fock` module and that of the :c:func:`scf` program. + The documentation of the :ref:`module_hartree_fock` module and that of the + :ref:`scf` program. This creates the |MOs| in the |EZFIO| database that will be used to perform any other post-SCF method. The |qp| does not handle symmetry and @@ -138,7 +139,7 @@ The estimated |FCI| energy of HCN is ``-93.0501`` au. .. seealso:: - The documentation of the :ref:`fci` module and that of the :c:func:`fci` program. + The documentation of the :ref:`module_fci` module and that of the :ref:`fci` program. --------------------------- diff --git a/man/cis.1 b/man/cis.1 index 07e3260b..7ecc6ace 100644 --- a/man/cis.1 +++ b/man/cis.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "CIS" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "CIS" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME cis \- | Quantum Package > . @@ -40,19 +40,24 @@ Disregarding spatial symmetry, it computes the \fIn_states\fP lowest eigenstates of that CI matrix. (see \fBdeterminants n_states\fP) .sp This program can be useful in many cases: +.INDENT 0.0 +.IP 1. 3 +Ground state calculation .sp To be sure to have the lowest SCF solution, perform an scf -(see the hartree_fock module), then a \fI\%cis\fP, save -the natural orbitals (see save_natorb) and re\-run an -scf optimization from this MO guess. +(see the module_hartree_fock module), then a \fI\%cis\fP, save the +natural orbitals (see save_natorb) and re\-run an scf +optimization from this MO guess. +.IP 2. 3 +Excited states calculations .sp The lowest excited states are much likely to be dominated by -single\-excitations. Therefore, running a \fI\%cis\fP will save -the \fIn_states\fP lowest states within the CIS space in the \fI\%EZFIO\fP +single\-excitations. Therefore, running a \fI\%cis\fP will save the +\fIn_states\fP lowest states within the CIS space in the \fI\%EZFIO\fP directory, which can afterwards be used as guess wave functions for -a further multi\-state FCI calculation if \fBdeterminants read_wf\fP -is set to \fBtrue\fP before running the fci -executable. +a further multi\-state FCI calculation if \fBdeterminants +read_wf\fP is set to \fBtrue\fP before running the fci executable. +.UNINDENT .sp If \fBdeterminants s2_eig\fP is set to \fBtrue\fP, the CIS will only retain states having the expected \ewidehat{S^2} value (see diff --git a/man/cisd.1 b/man/cisd.1 index 79bb7ae1..20954d68 100644 --- a/man/cisd.1 +++ b/man/cisd.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "CISD" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "CISD" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME cisd \- | Quantum Package > . @@ -43,17 +43,17 @@ matrix (see \fBdeterminants n_states\fP). This program can be useful in many cases: .INDENT 0.0 .IP \(bu 2 -GROUND STATE CALCULATION: if even after a \fBcis()\fP calculation, natural +\fBGround state calculation\fP: if even after a \fBcis()\fP calculation, natural orbitals (see \fBsave_natorb()\fP) and then \fBscf()\fP optimization, you are not sure to have the lowest scf solution, do the same strategy with the \fBcisd()\fP executable instead of the \fBcis()\fP\ exectuable to generate the natural orbitals as a guess for the \fBscf()\fP\&. .IP \(bu 2 -EXCITED STATES CALCULATIONS: the lowest excited states are much likely to +\fBExcited states calculations\fP: the lowest excited states are much likely to be dominanted by single\- or double\-excitations. Therefore, running a \fBcisd()\fP will save the “n_states” lowest states within the CISD space -in the EZFIO folder, which can afterward be used as guess wave functions +in the \fI\%EZFIO\fP directory, which can afterward be used as guess wave functions for a further multi\-state fci calculation if you specify “read_wf” = True before running the fci executable (see \fBdeterminants read_wf\fP). Also, if you specify “s2_eig” = True, the cisd will only retain states diff --git a/man/configure.1 b/man/configure.1 index 402f4cff..2bd704ed 100644 --- a/man/configure.1 +++ b/man/configure.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "CONFIGURE" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "CONFIGURE" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME configure \- | Quantum Package > . diff --git a/man/diagonalize_h.1 b/man/diagonalize_h.1 index 0579b2f0..ed8931ba 100644 --- a/man/diagonalize_h.1 +++ b/man/diagonalize_h.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "DIAGONALIZE_H" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "DIAGONALIZE_H" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME diagonalize_h \- | Quantum Package > . @@ -32,11 +32,13 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Program that extracts the \fBdeterminants n_states\fP lowest states of the Hamiltonian within the set of Slater determinants stored in the EZFIO folder. +Program that extracts the \fBdeterminants n_states\fP lowest +states of the Hamiltonian within the set of Slater determinants stored +in the \fI\%EZFIO\fP directory. .sp -If \fBdeterminants s2_eig\fP = True, it will retain only states -.sp -which corresponds to the desired value of \fBdeterminants expected_s2\fP\&. +If \fBdeterminants s2_eig\fP = \fBtrue\fP, it will retain only states +which correspond to the desired value of +\fBdeterminants expected_s2\fP\&. .sp Needs: .INDENT 0.0 diff --git a/man/excited_states.1 b/man/excited_states.1 index c35acce8..f96ab6f2 100644 --- a/man/excited_states.1 +++ b/man/excited_states.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "EXCITED_STATES" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "EXCITED_STATES" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME excited_states \- | Quantum Package > . diff --git a/man/fci.1 b/man/fci.1 index 0121e2ae..97975d6a 100644 --- a/man/fci.1 +++ b/man/fci.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "FCI" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "FCI" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME fci \- | Quantum Package > . @@ -46,7 +46,7 @@ conditions: .IP \(bu 2 number of Slater determinants > \fBdeterminants n_det_max\fP .IP \(bu 2 -PT2 < \fBperturbation pt2_max\fP +abs(PT2) less than \fBperturbation pt2_max\fP .UNINDENT .sp The following other options can be of interest: @@ -66,7 +66,7 @@ function with an \ewidehat{S^2} value corresponding to .UNINDENT .sp For excited states calculations, it is recommended to start with -\&.cis. or \&.cisd. guess wave functions, eventually in +cis or cisd guess wave functions, eventually in a restricted set of MOs, and to set \fBdeterminants s2_eig\fP to \fBtrue\fP\&. .sp diff --git a/man/fcidump.1 b/man/fcidump.1 index 6df57772..c8791248 100644 --- a/man/fcidump.1 +++ b/man/fcidump.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "FCIDUMP" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "FCIDUMP" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME fcidump \- | Quantum Package > . @@ -32,18 +32,22 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Produce a regular FCIDUMP file from the MOs stored in the \fI\%EZFIO\fP folder. +Produce a regular \fIFCIDUMP\fP file from the MOs stored in the \fI\%EZFIO\fP +directory. .sp -To specify an active space, the class of the mos have to set in the \fI\%EZFIO\fP folder (see qp_set_mo_class). +To specify an active space, the class of the MOs have to set in the +\fI\%EZFIO\fP directory (see qp_set_mo_class). .sp -The fcidump program supports 3 types of MO_class : +The \fI\%fcidump\fP program supports 3 types of MO classes : .INDENT 0.0 .IP \(bu 2 -the “core” orbitals which are always doubly occupied in the calculation +the \fIcore\fP orbitals which are always doubly occupied in the +calculation .IP \(bu 2 -the “del” orbitals that are never occupied in the calculation +the \fIdeleted\fP orbitals that are never occupied in the calculation .IP \(bu 2 -the “act” orbitals that will be occupied by a varying number of electrons +the \fIactive\fP orbitals that are occupied with a varying number of +electrons .UNINDENT .sp Needs: diff --git a/man/four_idx_transform.1 b/man/four_idx_transform.1 index cc610f5a..41f89b92 100644 --- a/man/four_idx_transform.1 +++ b/man/four_idx_transform.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "FOUR_IDX_TRANSFORM" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "FOUR_IDX_TRANSFORM" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME four_idx_transform \- | Quantum Package > . @@ -32,11 +32,14 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -4\-index transformation of two\-electron integrals from AO to MO integrals. +4\-index transformation of two\-electron integrals from AO to MO +integrals. .sp -This program will compute the two\-electron integrals on the MO basis and store it into the \fI\%EZFIO\fP folder. +This program will compute the two\-electron integrals on the MO basis +and store it into the \fI\%EZFIO\fP directory. .sp -This program can be useful if the AO –> MO transformation is an expensive step by itself. +This program can be useful if the AO –> MO transformation is an +expensive step by itself. .sp Needs: .INDENT 0.0 diff --git a/man/interfaces.1 b/man/interfaces.1 index 6b61eb4e..f9cadd99 100644 --- a/man/interfaces.1 +++ b/man/interfaces.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "INTERFACES" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "INTERFACES" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME interfaces \- | Quantum Package > . diff --git a/man/ks_scf.1 b/man/ks_scf.1 index e9eb6d53..00b42a45 100644 --- a/man/ks_scf.1 +++ b/man/ks_scf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "KS_SCF" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "KS_SCF" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME ks_scf \- | Quantum Package > . diff --git a/man/molden.1 b/man/molden.1 index 09ce8921..1ceae1ab 100644 --- a/man/molden.1 +++ b/man/molden.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "MOLDEN" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "MOLDEN" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME molden \- | Quantum Package > . @@ -32,7 +32,7 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Produce a Molden file +Produces a Molden file .sp Needs: .INDENT 0.0 diff --git a/man/natural_orbitals.1 b/man/natural_orbitals.1 index 8f8cf279..35b0980c 100644 --- a/man/natural_orbitals.1 +++ b/man/natural_orbitals.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "NATURAL_ORBITALS" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "NATURAL_ORBITALS" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME natural_orbitals \- | Quantum Package > . diff --git a/man/plugins.1 b/man/plugins.1 index 8107c596..018cf648 100644 --- a/man/plugins.1 +++ b/man/plugins.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PLUGINS" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "PLUGINS" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME plugins \- | Quantum Package > . diff --git a/man/print_e_conv.1 b/man/print_e_conv.1 index 2df9cc2d..21a083f1 100644 --- a/man/print_e_conv.1 +++ b/man/print_e_conv.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PRINT_E_CONV" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "PRINT_E_CONV" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME print_e_conv \- | Quantum Package > . diff --git a/man/print_wf.1 b/man/print_wf.1 index e0278254..515b8a91 100644 --- a/man/print_wf.1 +++ b/man/print_wf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PRINT_WF" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "PRINT_WF" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME print_wf \- | Quantum Package > . @@ -32,13 +32,15 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Print the ground state wave function stored in the \fI\%EZFIO\fP folder in the intermediate normalization. +Print the ground state wave function stored in the \fI\%EZFIO\fP directory +in the intermediate normalization. .sp -It also prints a lot of information regarding the excitation operators from the reference determinant +It also prints a lot of information regarding the excitation +operators from the reference determinant ! and a first\-order +perturbative analysis of the wave function. .sp -and a first\-order perturbative analysis of the wave function. -.sp -If the wave function strongly deviates from the first\-order analysis, something funny is going on :) +If the wave function strongly deviates from the first\-order analysis, +something funny is going on :) .sp Needs: .INDENT 0.0 diff --git a/man/printing.1 b/man/printing.1 index 2c9d32f1..0ba10e53 100644 --- a/man/printing.1 +++ b/man/printing.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PRINTING" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "PRINTING" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME printing \- | Quantum Package > . @@ -74,7 +74,7 @@ qp_run print_wf file.ezfio | tee file.ezfio.fci_natorb.wf .sp This program will, by default, print out the first 10^4 determinants whatever the size of the wave function stored in the -\fI\%EZFIO\fP folder. If you want to change the number of printed Slater +\fI\%EZFIO\fP directory. If you want to change the number of printed Slater determinants, just change the \fBdeterminants n_det_print_wf\fP keyword using the qp_edit tool. .sp diff --git a/man/pt2.1 b/man/pt2.1 index 743cbfed..91ac2941 100644 --- a/man/pt2.1 +++ b/man/pt2.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PT2" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "PT2" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME pt2 \- | Quantum Package > . @@ -32,13 +32,17 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Second order perturbative correction to the wave function contained in the EZFIO directory. +Second order perturbative correction to the wave function contained +in the \fI\%EZFIO\fP directory. .sp -This programs runs the stochastic PT2 correction on all “n_states” wave function stored in the EZFIO folder (see \fBdeterminant n_states\fP). +This programs runs the stochastic PT2 correction on all +\fBdeterminants n_states\fP wave functions stored in the \fI\%EZFIO\fP +directory. .sp -The option for the PT2 correction are the “pt2_relative_error” which is the relative stochastic -.sp -error on the PT2 to reach before stopping the stochastic sampling. (see \fBperturbation pt2_relative_error\fP) +The main option for the PT2 correction is the +\fBperturbation pt2_relative_error\fP which is the relative +stochastic error on the PT2 to reach before stopping the +sampling. .sp Needs: .INDENT 0.0 diff --git a/man/qp_convert_output_to_ezfio.1 b/man/qp_convert_output_to_ezfio.1 index 250852fc..43c10485 100644 --- a/man/qp_convert_output_to_ezfio.1 +++ b/man/qp_convert_output_to_ezfio.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_CONVERT_OUTPUT_TO_EZFIO" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_CONVERT_OUTPUT_TO_EZFIO" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_convert_output_to_ezfio \- | Quantum Package > . diff --git a/man/qp_create_ezfio_from_xyz.1 b/man/qp_create_ezfio_from_xyz.1 index 06e8a21c..de6a6da8 100644 --- a/man/qp_create_ezfio_from_xyz.1 +++ b/man/qp_create_ezfio_from_xyz.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_CREATE_EZFIO_FROM_XYZ" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_CREATE_EZFIO_FROM_XYZ" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_create_ezfio_from_xyz \- | Quantum Package > . diff --git a/man/qp_edit.1 b/man/qp_edit.1 index d1cded7f..3e222910 100644 --- a/man/qp_edit.1 +++ b/man/qp_edit.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_EDIT" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_EDIT" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_edit \- | Quantum Package > . diff --git a/man/qp_export_as_tgz.1 b/man/qp_export_as_tgz.1 index 0363eebb..0950a030 100644 --- a/man/qp_export_as_tgz.1 +++ b/man/qp_export_as_tgz.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_EXPORT_AS_TGZ" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_EXPORT_AS_TGZ" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_export_as_tgz \- | Quantum Package > . diff --git a/man/qp_plugins.1 b/man/qp_plugins.1 index 2a63d809..7e5db588 100644 --- a/man/qp_plugins.1 +++ b/man/qp_plugins.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_PLUGINS" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_PLUGINS" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_plugins \- | Quantum Package > . diff --git a/man/qp_reset.1 b/man/qp_reset.1 new file mode 100644 index 00000000..2b62d8ed --- /dev/null +++ b/man/qp_reset.1 @@ -0,0 +1,66 @@ +.\" Man page generated from reStructuredText. +. +.TH "QP_RESET" "1" "Jan 29, 2019" "2.0" "Quantum Package" +.SH NAME +qp_reset \- | Quantum Package > +. +.nr rst2man-indent-level 0 +. +.de1 rstReportMargin +\\$1 \\n[an-margin] +level \\n[rst2man-indent-level] +level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] +- +\\n[rst2man-indent0] +\\n[rst2man-indent1] +\\n[rst2man-indent2] +.. +.de1 INDENT +.\" .rstReportMargin pre: +. RS \\$1 +. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] +. nr rst2man-indent-level +1 +.\" .rstReportMargin post: +.. +.de UNINDENT +. RE +.\" indent \\n[an-margin] +.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] +.nr rst2man-indent-level -1 +.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] +.in \\n[rst2man-indent\\n[rst2man-indent-level]]u +.. +.sp +This command resets parts of the \fI\%EZFIO\fP directory. +.SH USAGE +.INDENT 0.0 +.INDENT 3.5 +.sp +.nf +.ft C +qp_reset [\-adhm] EZFIO_DIR +.ft P +.fi +.UNINDENT +.UNINDENT +.INDENT 0.0 +.TP +.B \-a, \-\-all +Reset to the state in which the directory is after after running qp_create_ezfio\&. +.UNINDENT +.INDENT 0.0 +.TP +.B \-d, \-\-dets +Deletes the determinants and CI coefficients. +.UNINDENT +.INDENT 0.0 +.TP +.B \-m, \-\-mos +Deletes the MOs, and consequently the determinants and CI coefficients. +.UNINDENT +.SH AUTHOR +A. Scemama, E. Giner +.SH COPYRIGHT +2019, A. Scemama, E. Giner +.\" Generated by docutils manpage writer. +. diff --git a/man/qp_run.1 b/man/qp_run.1 index 976a7318..7ec33303 100644 --- a/man/qp_run.1 +++ b/man/qp_run.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_RUN" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_RUN" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_run \- | Quantum Package > . diff --git a/man/qp_set_frozen_core.1 b/man/qp_set_frozen_core.1 index 24f87b09..7077976e 100644 --- a/man/qp_set_frozen_core.1 +++ b/man/qp_set_frozen_core.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_SET_FROZEN_CORE" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_SET_FROZEN_CORE" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_set_frozen_core \- | Quantum Package > . diff --git a/man/qp_set_mo_class.1 b/man/qp_set_mo_class.1 index a97f50e3..01c71fe6 100644 --- a/man/qp_set_mo_class.1 +++ b/man/qp_set_mo_class.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_SET_MO_CLASS" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_SET_MO_CLASS" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_set_mo_class \- | Quantum Package > . diff --git a/man/qp_stop.1 b/man/qp_stop.1 index 35fa3082..47cc7559 100644 --- a/man/qp_stop.1 +++ b/man/qp_stop.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_STOP" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_STOP" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_stop \- | Quantum Package > . diff --git a/man/qp_update.1 b/man/qp_update.1 index 4ee9654c..5acad761 100644 --- a/man/qp_update.1 +++ b/man/qp_update.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_UPDATE" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QP_UPDATE" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qp_update \- | Quantum Package > . diff --git a/man/qpsh.1 b/man/qpsh.1 index c445c006..e7f22a8c 100644 --- a/man/qpsh.1 +++ b/man/qpsh.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QPSH" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "QPSH" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME qpsh \- | Quantum Package > . @@ -153,7 +153,7 @@ qp (run|srun|mpirun) [options] .UNINDENT .UNINDENT .sp -Runs qp_run, qp_srun, or qp_mpirun using the current +Runs qp_run, \fBqp_srun\fP, or \fBqp_mpirun\fP using the current \fI\%EZFIO\fP directory. .UNINDENT .INDENT 0.0 diff --git a/man/rs_ks_scf.1 b/man/rs_ks_scf.1 index 2c7a715e..1fc27949 100644 --- a/man/rs_ks_scf.1 +++ b/man/rs_ks_scf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "RS_KS_SCF" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "RS_KS_SCF" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME rs_ks_scf \- | Quantum Package > . diff --git a/man/save_natorb.1 b/man/save_natorb.1 index b46fdad8..1b06061d 100644 --- a/man/save_natorb.1 +++ b/man/save_natorb.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "SAVE_NATORB" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "SAVE_NATORB" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME save_natorb \- | Quantum Package > . @@ -32,15 +32,16 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Save natural MOs into the EZFIO +Save natural MOs into the \fI\%EZFIO\fP\&. .sp -This program reads the wave function stored in the EZFIO folder, +This program reads the wave function stored in the \fI\%EZFIO\fP directory, +extracts the corresponding natural orbitals and setd them as the new +MOs\&. .sp -extracts the corresponding natural orbitals and set them as the new MOs -.sp -If this is a multi\-state calculation, the density matrix that produces the natural orbitals -.sp -is obtained from a state\-averaged of the density matrices of each state with the corresponding state_average_weight (see the doc of state_average_weight). +If this is a multi\-state calculation, the density matrix that produces +the natural orbitals is obtained from an average of the density +matrices of each state with the corresponding +\fBdeterminants state_average_weight\fP .sp Needs: .INDENT 0.0 diff --git a/man/save_one_e_dm.1 b/man/save_one_e_dm.1 index 80fb6ff2..5899cdfb 100644 --- a/man/save_one_e_dm.1 +++ b/man/save_one_e_dm.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "SAVE_ONE_E_DM" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "SAVE_ONE_E_DM" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME save_one_e_dm \- | Quantum Package > . @@ -32,12 +32,16 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -programs that computes the one body density on the mo basis for alpha and beta electrons -from the wave function stored in the EZFIO folder, and then save it into the EZFIO folder aux_quantities. +Program that computes the one body density on the MO basis +for $alpha$ and $beta$ electrons from the wave function +stored in the \fI\%EZFIO\fP directory, and then saves it into the +module_aux_quantities\&. .sp -Then, the global variable data_one_e_dm_alpha_mo and data_one_e_dm_beta_mo will automatically read this density in a further calculation. -.sp -This can be used to perform damping on the density in RS\-DFT calculation (see the density_for_dft module). +Then, the global variable \fBaux_quantities data_one_e_dm_alpha_mo\fP +and \fBaux_quantities data_one_e_dm_beta_mo\fP will automatically +read this density in the next calculation. This can be used to perform +damping on the density in RSDFT calculations (see +module_density_for_dft). .sp Needs: .INDENT 0.0 diff --git a/man/save_ortho_mos.1 b/man/save_ortho_mos.1 index 0cdfc0ce..a3183723 100644 --- a/man/save_ortho_mos.1 +++ b/man/save_ortho_mos.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "SAVE_ORTHO_MOS" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "SAVE_ORTHO_MOS" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME save_ortho_mos \- | Quantum Package > . diff --git a/man/scf.1 b/man/scf.1 index cc0d3b14..9ff63737 100644 --- a/man/scf.1 +++ b/man/scf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "SCF" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "SCF" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME scf \- | Quantum Package > . diff --git a/man/write_integrals_erf.1 b/man/write_integrals_erf.1 index 45689b7b..71b989c6 100644 --- a/man/write_integrals_erf.1 +++ b/man/write_integrals_erf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "WRITE_INTEGRALS_ERF" "1" "Jan 25, 2019" "2.0" "Quantum Package" +.TH "WRITE_INTEGRALS_ERF" "1" "Jan 29, 2019" "2.0" "Quantum Package" .SH NAME write_integrals_erf \- | Quantum Package > . @@ -32,7 +32,8 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Saves the two\-electron integrals with the erf(\emu r_{12})/r_{12} oprerator into the EZFIO folder +Saves the two\-electron integrals with the $erf(mu r_{12})/r_{12}$ +oprerator into the EZFIO directory. .sp Needs: .INDENT 0.0 diff --git a/src/ao_basis/README.rst b/src/ao_basis/README.rst index 753dd12b..6adfdd82 100644 --- a/src/ao_basis/README.rst +++ b/src/ao_basis/README.rst @@ -17,9 +17,13 @@ The |AO| coefficients are normalized as: {\tilde c}_{ki} = \frac{c_{ki}}{ \int \left( (x-X_A)^a (y-Y_A)^b (z-Z_A)^c e^{-\gamma_{ki} |{\bf r} - {\bf R}_A|^2} \right)^2 dr} -Warning: `ao_coef` contains the |AO| coefficients given in input. These do not -include the normalization constant of the |AO|. The `ao_coef_normalized` provider includes -this normalization factor. + +.. warning:: + + `ao_coef` contains the |AO| coefficients given in input. These do not + include the normalization constant of the |AO|. The `ao_coef_normalized` + provider includes this normalization factor. + The |AOs| are also sorted by increasing exponent to accelerate the calculation of the two electron integrals. diff --git a/src/ao_basis/aos_in_r.irp.f b/src/ao_basis/aos_in_r.irp.f index 1370d4bc..88149c92 100644 --- a/src/ao_basis/aos_in_r.irp.f +++ b/src/ao_basis/aos_in_r.irp.f @@ -1,7 +1,7 @@ double precision function ao_value(i,r) implicit none BEGIN_DOC -! return the value of the ith ao at point r +! Returns the value of the i-th ao at point $\textbf{r}$ END_DOC double precision, intent(in) :: r(3) integer, intent(in) :: i @@ -35,7 +35,8 @@ end double precision function primitive_value(i,j,r) implicit none BEGIN_DOC -! return the value of the jth primitive of ith ao at point r WITHOUT THE COEF +! Returns the value of the j-th primitive of the i-th |AO| at point $\textbf{r} +! **without the coefficient** END_DOC double precision, intent(in) :: r(3) integer, intent(in) :: i,j @@ -68,7 +69,7 @@ end subroutine give_all_aos_at_r_old(r,aos_array) implicit none BEGIN_dOC -! gives the values of aos at a given point r +! Gives the values of |AOs| at a given point $\textbf{r}$ END_DOC double precision, intent(in) :: r(3) double precision, intent(out) :: aos_array(ao_num) @@ -83,8 +84,9 @@ end subroutine give_all_aos_at_r(r,aos_array) implicit none BEGIN_dOC -! input : r == r(1) = x and so on -! aos_array(i) = aos(i) evaluated in r +! input : r == r(1) = x and so on +! +! output : aos_array(i) = aos(i) evaluated in $\textbf{r}$ END_DOC double precision, intent(in) :: r(3) double precision, intent(out) :: aos_array(ao_num) @@ -121,9 +123,13 @@ end subroutine give_all_aos_and_grad_at_r(r,aos_array,aos_grad_array) implicit none BEGIN_DOC -! input : r(1) ==> r(1) = x, r(2) = y, r(3) = z -! output : aos_array(i) = ao(i) evaluated at r -! : aos_grad_array(1,i) = gradient X of the ao(i) evaluated at r +! input : r(1) ==> r(1) = x, r(2) = y, r(3) = z +! +! output : +! +! * aos_array(i) = ao(i) evaluated at ro +! * aos_grad_array(1,i) = gradient X of the ao(i) evaluated at $\textbf{r}$ +! END_DOC double precision, intent(in) :: r(3) double precision, intent(out) :: aos_array(ao_num) @@ -187,9 +193,12 @@ end subroutine give_all_aos_and_grad_and_lapl_at_r(r,aos_array,aos_grad_array,aos_lapl_array) implicit none BEGIN_DOC -! input : r(1) ==> r(1) = x, r(2) = y, r(3) = z -! output : aos_array(i) = ao(i) evaluated at r -! : aos_grad_array(1,i) = gradient X of the ao(i) evaluated at r +! input : r(1) ==> r(1) = x, r(2) = y, r(3) = z +! +! output : +! +! * aos_array(i) = ao(i) evaluated at $\textbf{r}$ +! * aos_grad_array(1,i) = $\nabla_x$ of the ao(i) evaluated at $\textbf{r}$ END_DOC double precision, intent(in) :: r(3) double precision, intent(out) :: aos_array(ao_num) diff --git a/src/ao_one_e_ints/kin_ao_ints.irp.f b/src/ao_one_e_ints/kin_ao_ints.irp.f index 8e981d77..b87e2a22 100644 --- a/src/ao_one_e_ints/kin_ao_ints.irp.f +++ b/src/ao_one_e_ints/kin_ao_ints.irp.f @@ -5,8 +5,10 @@ BEGIN_DOC ! Second derivative matrix elements in the |AO| basis. ! - ! :math:`{\tt ao\_deriv2\_x} = - ! \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle` + ! .. math:: + ! + ! {\tt ao\_deriv2\_x} = + ! \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle ! END_DOC integer :: i,j,n,l @@ -122,7 +124,8 @@ BEGIN_PROVIDER [double precision, ao_kinetic_integrals, (ao_num,ao_num)] BEGIN_DOC ! Kinetic energy integrals in the |AO| basis. ! - ! :math:`\langle \chi_i |\hat{T}| \chi_j \rangle` + ! $\langle \chi_i |\hat{T}| \chi_j \rangle$ + ! END_DOC integer :: i,j,k,l diff --git a/src/ao_one_e_ints/pot_ao_erf_ints.irp.f b/src/ao_one_e_ints/pot_ao_erf_ints.irp.f index 66637420..42505194 100644 --- a/src/ao_one_e_ints/pot_ao_erf_ints.irp.f +++ b/src/ao_one_e_ints/pot_ao_erf_ints.irp.f @@ -2,7 +2,7 @@ subroutine give_all_erf_kl_ao(integrals_ao,mu_in,C_center) implicit none BEGIN_DOC ! Subroutine that returns all integrals over $r$ of type - ! $\frac{ \erf(\mu * |r-R_C|) }{ |r-R_C| }$ + ! $\frac{ \erf(\mu * | r - R_C | ) }{ | r - R_C | }$ END_DOC double precision, intent(in) :: mu_in,C_center(3) double precision, intent(out) :: integrals_ao(ao_num,ao_num) @@ -20,7 +20,7 @@ double precision function NAI_pol_mult_erf_ao(i_ao,j_ao,mu_in,C_center) implicit none BEGIN_DOC ! Computes the following integral : - ! $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) \frac{\erf(\mu |r-R_C|)}{|r-R_C|}$. + ! $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) \frac{\erf(\mu | r - R_C | )}{ | r - R_C | }$. END_DOC integer, intent(in) :: i_ao,j_ao double precision, intent(in) :: mu_in, C_center(3) @@ -51,8 +51,12 @@ end double precision function NAI_pol_mult_erf(A_center,B_center,power_A,power_B,alpha,beta,C_center,n_pt_in,mu_in) BEGIN_DOC ! Computes the following integral : - ! $\int dr (x-A_x)^a (x-B_x)^b \exp(-\alpha (x-A_x)^2 - \beta (x-B_x)^2 ) - ! \frac{\erf(\mu |r-R_C|)}{|r-R_c|}$. + ! + ! .. math:: + ! + ! \int dr (x-A_x)^a (x-B_x)^b \exp(-\alpha (x-A_x)^2 - \beta (x-B_x)^2 ) + ! \frac{\erf(\mu | r - R_C | )}{ | r - R_C | }$. + ! END_DOC implicit none @@ -126,7 +130,8 @@ end subroutine give_polynomial_mult_center_one_e_erf_opt(A_center,B_center,alpha,beta,& power_A,power_B,C_center,n_pt_in,d,n_pt_out,mu_in,p,p_inv,p_inv_2,p_new,P_center) BEGIN_DOC - ! Returns the explicit polynomial in terms of the $t$ variable of the following polynomial: + ! Returns the explicit polynomial in terms of the $t$ variable of the + ! following polynomial: ! ! $I_{x1}(a_x, d_x,p,q) \times I_{x1}(a_y, d_y,p,q) \times I_{x1}(a_z, d_z,p,q)$. END_DOC @@ -244,7 +249,8 @@ end subroutine give_polynomial_mult_center_one_e_erf(A_center,B_center,alpha,beta,& power_A,power_B,C_center,n_pt_in,d,n_pt_out,mu_in) BEGIN_DOC - ! Returns the explicit polynomial in terms of the $t$ variable of the following polynomial: + ! Returns the explicit polynomial in terms of the $t$ variable of the + ! following polynomial: ! ! $I_{x1}(a_x, d_x,p,q) \times I_{x1}(a_y, d_y,p,q) \times I_{x1}(a_z, d_z,p,q)$. END_DOC @@ -262,7 +268,6 @@ subroutine give_polynomial_mult_center_one_e_erf(A_center,B_center,alpha,beta,& double precision :: accu, pq_inv, p10_1, p10_2, p01_1, p01_2 double precision :: p,P_center(3),rho,p_inv,p_inv_2 accu = 0.d0 - !COMPTEUR irp_rdtsc1 = irp_rdtsc() ASSERT (n_pt_in > 1) p = alpha+beta p_inv = 1.d0/p diff --git a/src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f b/src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f index 24a48e32..4433690f 100644 --- a/src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f +++ b/src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f @@ -458,11 +458,13 @@ end double precision function ERI_erf(alpha,beta,delta,gama,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z) implicit none BEGIN_DOC - ! ATOMIC PRIMTIVE two-electron integral between the 4 primitives :: - ! primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2) - ! primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2) - ! primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2) - ! primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2) + ! Atomic primtive two-electron integral between the 4 primitives : + ! + ! * primitive 1 : $x_1^{a_x} y_1^{a_y} z_1^{a_z} \exp(-\alpha * r1^2)$ + ! * primitive 2 : $x_1^{b_x} y_1^{b_y} z_1^{b_z} \exp(- \beta * r1^2)$ + ! * primitive 3 : $x_2^{c_x} y_2^{c_y} z_2^{c_z} \exp(-\delta * r2^2)$ + ! * primitive 4 : $x_2^{d_x} y_2^{d_y} z_2^{d_z} \exp(-\gamma * r2^2)$ + ! END_DOC double precision, intent(in) :: delta,gama,alpha,beta integer, intent(in) :: a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z @@ -517,9 +519,11 @@ end subroutine integrale_new_erf(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt) BEGIN_DOC - ! calculate the integral of the polynom :: - ! I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q) - ! between ( 0 ; 1) + ! Calculate the integral of the polynomial : + ! + ! $I_x1(a_x+b_x, c_x+d_x,p,q) \, I_x1(a_y+b_y, c_y+d_y,p,q) \, I_x1(a_z+b_z, c_z+d_z,p,q)$ + ! + ! between $( 0 ; 1)$ END_DOC diff --git a/src/ao_two_e_ints/two_e_integrals.irp.f b/src/ao_two_e_ints/two_e_integrals.irp.f index ca3b950d..3ecdbbb2 100644 --- a/src/ao_two_e_ints/two_e_integrals.irp.f +++ b/src/ao_two_e_ints/two_e_integrals.irp.f @@ -641,9 +641,10 @@ end subroutine integrale_new(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt) BEGIN_DOC - ! calculate the integral of the polynom :: - ! I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q) - ! between ( 0 ; 1) + ! Calculates the integral of the polynomial : + ! + ! $I_{x_1}(a_x+b_x,c_x+d_x,p,q) \, I_{x_1}(a_y+b_y,c_y+d_y,p,q) \, I_{x_1}(a_z+b_z,c_z+d_z,p,q)$ + ! in $( 0 ; 1)$ END_DOC @@ -775,8 +776,9 @@ integer function n_pt_sup(a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z) implicit none BEGIN_DOC ! Returns the upper boundary of the degree of the polynomial involved in the - ! bielctronic integral : - ! Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z) + ! two-electron integral : + ! + ! $I_x(a_x,b_x,c_x,d_x) \, I_y(a_y,b_y,c_y,d_y) \, I_z(a_z,b_z,c_z,d_z)$ END_DOC integer :: a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z n_pt_sup = shiftl( a_x+b_x+c_x+d_x + a_y+b_y+c_y+d_y + a_z+b_z+c_z+d_z,1 ) @@ -790,7 +792,8 @@ subroutine give_polynom_mult_center_x(P_center,Q_center,a_x,d_x,p,q,n_pt_in,pq_i BEGIN_DOC ! subroutine that returns the explicit polynom in term of the "t" ! variable of the following polynomw : - ! I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q) + ! + ! $I_{x_1}(a_x,d_x,p,q) \, I_{x_1}(a_y,d_y,p,q) \ I_{x_1}(a_z,d_z,p,q)$ END_DOC integer, intent(in) :: n_pt_in integer,intent(out) :: n_pt_out @@ -851,7 +854,7 @@ end subroutine I_x1_pol_mult(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in) implicit none BEGIN_DOC - ! recursive function involved in the two-electron integral + ! Recursive function involved in the two-electron integral END_DOC integer , intent(in) :: n_pt_in include 'utils/constants.include.F' @@ -885,7 +888,7 @@ end recursive subroutine I_x1_pol_mult_recurs(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in) implicit none BEGIN_DOC - ! recursive function involved in the two-electron integral + ! Recursive function involved in the two-electron integral END_DOC integer , intent(in) :: n_pt_in include 'utils/constants.include.F' @@ -966,7 +969,7 @@ end recursive subroutine I_x1_pol_mult_a1(c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in) implicit none BEGIN_DOC - ! recursive function involved in the two-electron integral + ! Recursive function involved in the two-electron integral END_DOC integer , intent(in) :: n_pt_in include 'utils/constants.include.F' @@ -1017,7 +1020,7 @@ end recursive subroutine I_x1_pol_mult_a2(c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt_in) implicit none BEGIN_DOC - ! recursive function involved in the two-electron integral + ! Recursive function involved in the two-electron integral END_DOC integer , intent(in) :: n_pt_in include 'utils/constants.include.F' @@ -1075,7 +1078,7 @@ end recursive subroutine I_x2_pol_mult(c,B_10,B_01,B_00,C_00,D_00,d,nd,dim) implicit none BEGIN_DOC - ! recursive function involved in the two-electron integral + ! Recursive function involved in the two-electron integral END_DOC integer , intent(in) :: dim include 'utils/constants.include.F' diff --git a/src/aux_quantities/README.rst b/src/aux_quantities/README.rst index 62036952..c2b8b5ed 100644 --- a/src/aux_quantities/README.rst +++ b/src/aux_quantities/README.rst @@ -4,18 +4,19 @@ aux_quantities This module contains some global variables (such as densities and energies) -which are stored in the EZFIO folder in a different place than determinants. +which are stored in the |EZFIO| directory in a different place than determinants. This is used in practice to store density matrices which can be obtained from -any methods, as long as they are stored in the same MO basis which is used for +any method, as long as they are stored in the same |MO| basis which is used for the calculations. In |RSDFT| calculations, this can be done to perform damping -on the density in order to speed up convergence. +on the density in order to speed up the convergence. The main providers of that module are: -* `data_one_e_dm_alpha_mo` and `data_one_e_dm_beta_mo` which are the - one-body alpha and beta densities which are necessary read from the EZFIO - folder. +* :c:data:`data_one_e_dm_alpha_mo` and :c:data:`data_one_e_dm_beta_mo` which + are the one-body alpha and beta densities which are necessary read from the + |EZFIO| directory. Thanks to these providers you can use any density matrix that does not -necessary corresponds to that of the current wave function. +necessarily corresponds to that of the current wave function. + diff --git a/src/cipsi/README.rst b/src/cipsi/README.rst index 401c0cc6..054f938f 100644 --- a/src/cipsi/README.rst +++ b/src/cipsi/README.rst @@ -43,7 +43,7 @@ By default, the program will stop when more than one million determinants have been selected, or when the |PT2| energy is below :math:`10^{-4}`. The variational and |PT2| energies of the iterations are stored in the -|EZFIO| database, in the :ref:`iterations` module. +|EZFIO| database, in the :ref:`module_iterations` module. diff --git a/src/cipsi/pt2_stoch_routines.irp.f b/src/cipsi/pt2_stoch_routines.irp.f index a994d331..d93d977a 100644 --- a/src/cipsi/pt2_stoch_routines.irp.f +++ b/src/cipsi/pt2_stoch_routines.irp.f @@ -330,8 +330,7 @@ subroutine pt2_slave_inproc(i) end -subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error, & - variance, norm, b, N_) +subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error, variance, norm, b, N_) use f77_zmq use selection_types use bitmasks diff --git a/src/cis/README.rst b/src/cis/README.rst index b1e3e2e1..61077e69 100644 --- a/src/cis/README.rst +++ b/src/cis/README.rst @@ -2,34 +2,39 @@ cis === -This module contains a CIS program. +This module contains a |CIS| program. The user point of view ---------------------- -The :command:`cis` program performs the CI of the ROHF-like + all single excitations on top of it. -This program can be very useful to : +The :ref:`cis` program performs the CI to obtain the ROHF reference + all +single excitations on top of it. This program can be very useful to: -* **Ground state calculations**: generate a guess for the ground state wave function if one is not sure that the :c:func:`scf` program gave the lowest SCF solution. In combination with :c:func:`save_natorb` it can produce new |MOs| in order to reperform an :c:func:`scf` optimization. +* **Ground state calculations**: generate a guess for the ground state wave + function if one is not sure that the :ref:`scf` program gave the lowest |SCF| + solution. In combination with :ref:`save_natorb` it can produce new |MOs| in + order to reperform an :ref:`scf` optimization. -* **Excited states calculations**: generate guess for all the :option:`determinants n_states` wave functions, that will be used by the :c:func:`fci` program. +* **Excited states calculations**: generate guesses for all the + :option:`determinants n_states` wave functions, that will be used by the + :ref:`fci` program. The main keywords/options to be used are: -* :option:`determinants n_states` : number of states to consider for the |CIS| calculation +* :option:`determinants n_states`: number of states to consider for the |CIS| calculation -* :option:`determinants s2_eig` : force all states to have the desired value of :math:`S^2` +* :option:`determinants s2_eig`: force all states to have the desired value of |S^2| -* :option:`determinants expected_s2` : desired value of :math:`S^2` +* :option:`determinants expected_s2`: desired value of |S^2| -The programmer point of view ----------------------------- +The programmer's point of view +------------------------------ -This module have been built by setting the following rules: +This module was built by setting the following rules: * The only generator determinant is the Hartree-Fock (single-reference method) * All generated singly excited determinants are included in the wave function (no perturbative diff --git a/src/cis/cis.irp.f b/src/cis/cis.irp.f index 6ab2e7e9..48f0b9e5 100644 --- a/src/cis/cis.irp.f +++ b/src/cis/cis.irp.f @@ -1,55 +1,52 @@ program cis implicit none BEGIN_DOC - ! - ! Configuration Interaction with Single excitations. - ! - ! This program takes a reference Slater determinant of ROHF-like - ! occupancy, and performs all single excitations on top of it. - ! Disregarding spatial symmetry, it computes the `n_states` lowest - ! eigenstates of that CI matrix. (see :option:`determinants n_states`) - ! - ! This program can be useful in many cases: - ! - ! - ! Ground state calculation - ! ------------------------ - ! - ! To be sure to have the lowest |SCF| solution, perform an :ref:`scf` - ! (see the :ref:`hartree_fock` module), then a :ref:`cis`, save - ! the natural orbitals (see :ref:`save_natorb`) and re-run an - ! :ref:`scf` optimization from this |MO| guess. - ! - ! - ! Excited states calculations - ! --------------------------- - ! - ! The lowest excited states are much likely to be dominated by - ! single-excitations. Therefore, running a :ref:`cis` will save - ! the `n_states` lowest states within the |CIS| space in the |EZFIO| - ! directory, which can afterwards be used as guess wave functions for - ! a further multi-state |FCI| calculation if :option:`determinants read_wf` - ! is set to |true| before running the :ref:`fci` - ! executable. - ! - ! - ! If :option:`determinants s2_eig` is set to |true|, the |CIS| - ! will only retain states having the expected |S^2| value (see - ! :option:`determinants expected_s2`). Otherwise, the |CIS| will take - ! the lowest :option:`determinants n_states`, whatever multiplicity - ! they are. - ! - ! .. note:: - ! - ! To discard some orbitals, use the :ref:`qp_set_mo_class` - ! command to specify: - ! - ! * *core* orbitals which will be always doubly occupied - ! - ! * *act* orbitals where an electron can be either excited from or to - ! - ! * *del* orbitals which will be never occupied - ! +! +! Configuration Interaction with Single excitations. +! +! This program takes a reference Slater determinant of ROHF-like +! occupancy, and performs all single excitations on top of it. +! Disregarding spatial symmetry, it computes the `n_states` lowest +! eigenstates of that CI matrix. (see :option:`determinants n_states`) +! +! This program can be useful in many cases: +! +! +! 1. Ground state calculation +! +! To be sure to have the lowest |SCF| solution, perform an :ref:`scf` +! (see the :ref:`module_hartree_fock` module), then a :ref:`cis`, save the +! natural orbitals (see :ref:`save_natorb`) and re-run an :ref:`scf` +! optimization from this |MO| guess. +! +! +! 2. Excited states calculations +! +! The lowest excited states are much likely to be dominated by +! single-excitations. Therefore, running a :ref:`cis` will save the +! `n_states` lowest states within the |CIS| space in the |EZFIO| +! directory, which can afterwards be used as guess wave functions for +! a further multi-state |FCI| calculation if :option:`determinants +! read_wf` is set to |true| before running the :ref:`fci` executable. +! +! +! If :option:`determinants s2_eig` is set to |true|, the |CIS| +! will only retain states having the expected |S^2| value (see +! :option:`determinants expected_s2`). Otherwise, the |CIS| will take +! the lowest :option:`determinants n_states`, whatever multiplicity +! they are. +! +! .. note:: +! +! To discard some orbitals, use the :ref:`qp_set_mo_class` +! command to specify: +! +! * *core* orbitals which will be always doubly occupied +! +! * *act* orbitals where an electron can be either excited from or to +! +! * *del* orbitals which will be never occupied +! END_DOC read_wf = .False. SOFT_TOUCH read_wf diff --git a/src/cisd/cisd.irp.f b/src/cisd/cisd.irp.f index e21423cf..9631f971 100644 --- a/src/cisd/cisd.irp.f +++ b/src/cisd/cisd.irp.f @@ -11,7 +11,7 @@ program cisd ! ! This program can be useful in many cases: ! - ! * GROUND STATE CALCULATION: if even after a :c:func:`cis` calculation, natural + ! * **Ground state calculation**: if even after a :c:func:`cis` calculation, natural ! orbitals (see :c:func:`save_natorb`) and then :c:func:`scf` optimization, you are not sure to have the lowest scf ! solution, ! do the same strategy with the :c:func:`cisd` executable instead of the :c:func:`cis` exectuable to generate the natural @@ -19,11 +19,11 @@ program cisd ! ! ! - ! * EXCITED STATES CALCULATIONS: the lowest excited states are much likely to + ! * **Excited states calculations**: the lowest excited states are much likely to ! be dominanted by single- or double-excitations. ! Therefore, running a :c:func:`cisd` will save the "n_states" lowest states within ! the CISD space - ! in the EZFIO folder, which can afterward be used as guess wave functions + ! in the |EZFIO| directory, which can afterward be used as guess wave functions ! for a further multi-state fci calculation if you specify "read_wf" = True ! before running the fci executable (see :option:`determinants read_wf`). ! Also, if you specify "s2_eig" = True, the cisd will only retain states diff --git a/src/davidson/README.rst b/src/davidson/README.rst index 596abca0..1df5f343 100644 --- a/src/davidson/README.rst +++ b/src/davidson/README.rst @@ -3,12 +3,19 @@ davidson ======== Abstract module for Davidson's diagonalization. -It contains everything required for the Davidson algorithm, dressed or not. If -a dressing is used, the dressing column should be defined and the -:ref:`davidson_dressed` module should be used. If no dressing is required, -the :ref:`davidson` module should be used, and it has a default zero dressing vector. +It contains everything required for the Davidson algorithm, dressed or +not. If a dressing is used, the dressing column should be defined and +the :ref:`module_davidson_dressed` module should be used. If no dressing +is required, the :ref:`module_davidson` module should be used, and it +has a default zero dressing vector. The important providers for that module are: -# `psi_energy` which is the expectation value over the wave function (`psi_det`, `psi_coef`) of the Hamiltonian, dressed or not. It uses the general subroutine `u_0_H_u_0`. -# `psi_energy_two_e` which is the expectation value over the wave function (`psi_det`, `psi_coef`) of the standard two-electrons coulomb operator. It uses the general routine `u_0_H_u_0_two_e`. +#. :c:data:`psi_energy` which is the expectation value over the wave + function (:c:data:`psi_det`, :c:data:`psi_coef`) of the Hamiltonian, + dressed or not. It uses the general subroutine :c:func:`u_0_H_u_0`. + +#. :c:data:`psi_energy_two_e` which is the expectation value over the + wave function (:c:data:`psi_det`, :c:data:`psi_coef`) of the standard + two-electron Coulomb operator. It uses the general routine + :c:func:`u_0_H_u_0_two_e`. diff --git a/src/davidson/davidson_parallel.irp.f b/src/davidson/davidson_parallel.irp.f index a1f69841..f8c17344 100644 --- a/src/davidson/davidson_parallel.irp.f +++ b/src/davidson/davidson_parallel.irp.f @@ -51,6 +51,12 @@ subroutine davidson_run_slave(thread,iproc) doexit=1 endif endif + doexit = receive + IRP_ENDIF + if (doexit>0) then + call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) + return + endif IRP_IF MPI include 'mpif.h' @@ -187,7 +193,7 @@ subroutine davidson_push_results(zmq_socket_push, v_t, s_t, imin, imax, task_id) use f77_zmq implicit none BEGIN_DOC -! Push the results of $H|U \rangle$ from a worker to the master. +! Push the results of $H | U \rangle$ from a worker to the master. END_DOC integer(ZMQ_PTR) ,intent(in) :: zmq_socket_push @@ -233,7 +239,7 @@ subroutine davidson_pull_results(zmq_socket_pull, v_t, s_t, imin, imax, task_id) use f77_zmq implicit none BEGIN_DOC -! Pull the results of $H|U \rangle$ on the master. +! Pull the results of $H | U \rangle$ on the master. END_DOC integer(ZMQ_PTR) ,intent(in) :: zmq_socket_pull @@ -324,13 +330,13 @@ subroutine H_S2_u_0_nstates_zmq(v_0,s_0,u_0,N_st,sze) use f77_zmq implicit none BEGIN_DOC - ! Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$ + ! Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2 | u_0\rangle$ ! ! n : number of determinants ! - ! H_jj : array of $\langle j|H|j \rangle$ + ! H_jj : array of $\langle j | H | j \rangle$ ! - ! S2_jj : array of $\langle j|S^2|j \rangle$ + ! S2_jj : array of $\langle j | S^2 | j \rangle$ END_DOC integer, intent(in) :: N_st, sze double precision, intent(out) :: v_0(sze,N_st), s_0(sze,N_st) diff --git a/src/davidson/u0_h_u0.irp.f b/src/davidson/u0_h_u0.irp.f index f2f87b84..c55cb631 100644 --- a/src/davidson/u0_h_u0.irp.f +++ b/src/davidson/u0_h_u0.irp.f @@ -27,9 +27,9 @@ subroutine u_0_H_u_0(e_0,s_0,u_0,n,keys_tmp,Nint,N_st,sze) use bitmasks implicit none BEGIN_DOC - ! Computes $E_0 = \frac{\langle u_0|H|u_0 \rangle}{\langle u_0|u_0 \rangle}$ + ! Computes $E_0 = \frac{\langle u_0 | H | u_0 \rangle}{\langle u_0 | u_0 \rangle}$ ! - ! and $S_0 = \frac{\langle u_0|S^2|u_0 \rangle}{\langle u_0|u_0 \rangle}$ + ! and $S_0 = \frac{\langle u_0 | S^2 | u_0 \rangle}{\langle u_0 | u_0 \rangle}$ ! ! n : number of determinants ! @@ -80,7 +80,7 @@ subroutine H_S2_u_0_nstates_openmp(v_0,s_0,u_0,N_st,sze) use bitmasks implicit none BEGIN_DOC - ! Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$. + ! Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2 | u_0\rangle$. ! ! Assumes that the determinants are in psi_det ! @@ -135,7 +135,7 @@ subroutine H_S2_u_0_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,ishift, use bitmasks implicit none BEGIN_DOC - ! Computes $v_t = H|u_t\rangle$ and $s_t = S^2 |u_t\rangle$ + ! Computes $v_t = H | u_t\rangle$ and $s_t = S^2 | u_t\rangle$ ! ! Default should be 1,N_det,0,1 END_DOC @@ -165,7 +165,7 @@ subroutine H_S2_u_0_nstates_openmp_work_$N_int(v_t,s_t,u_t,N_st,sze,istart,iend, use bitmasks implicit none BEGIN_DOC - ! Computes $v_t = H|u_t\rangle$ and $s_t = S^2 |u_t\rangle$ + ! Computes $v_t = H | u_t \\rangle$ and $s_t = S^2 | u_t\\rangle$ ! ! Default should be 1,N_det,0,1 END_DOC diff --git a/src/davidson/u0_wee_u0.irp.f b/src/davidson/u0_wee_u0.irp.f index 8b071629..1b16bfa1 100644 --- a/src/davidson/u0_wee_u0.irp.f +++ b/src/davidson/u0_wee_u0.irp.f @@ -15,7 +15,7 @@ subroutine H_S2_u_0_two_e_nstates_openmp(v_0,s_0,u_0,N_st,sze) use bitmasks implicit none BEGIN_DOC - ! Computes $v_0 = H|u_0\rangle$ and $s_0 = S^2 |u_0\rangle$ + ! Computes $v_0 = H | u_0\rangle$ and $s_0 = S^2 | u_0\rangle$ ! ! Assumes that the determinants are in psi_det ! @@ -69,7 +69,7 @@ subroutine H_S2_u_0_two_e_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,i use bitmasks implicit none BEGIN_DOC - ! Computes $v_t = H|u_t\rangle$ and $s_t = S^2 |u_t\rangle$ + ! Computes $v_t = H | u_t\rangle$ and $s_t = S^2 | u_t\rangle$ ! ! Default should be 1,N_det,0,1 END_DOC @@ -99,7 +99,7 @@ subroutine H_S2_u_0_two_e_nstates_openmp_work_$N_int(v_t,s_t,u_t,N_st,sze,istart use bitmasks implicit none BEGIN_DOC - ! Computes $v_t = H|u_t\rangle$ and $s_t = S^2 |u_t\rangle$ + ! Computes $v_t = H | u_t \\rangle$ and $s_t = S^2 | u_t \\rangle$ ! ! Default should be 1,N_det,0,1 END_DOC @@ -461,7 +461,7 @@ subroutine u_0_H_u_0_two_e(e_0,u_0,n,keys_tmp,Nint,N_st,sze) use bitmasks implicit none BEGIN_DOC - ! Computes $E_0 = \frac{ \langle u_0|H|u_0\rangle}{\langle u_0|u_0 \rangle}$. + ! Computes $E_0 = \frac{ \langle u_0 | H | u_0\rangle}{\langle u_0 | u_0 \rangle}$. ! ! n : number of determinants ! diff --git a/src/density_for_dft/README.rst b/src/density_for_dft/README.rst index 278a27ef..612d236e 100644 --- a/src/density_for_dft/README.rst +++ b/src/density_for_dft/README.rst @@ -3,10 +3,14 @@ density_for_dft =============== -This module defines the *provider* of the density used for the DFT related calculations. -This definition is done through the keyword :option:`density_for_dft density_for_dft`. -The density can be: +This module defines the *provider* of the density used for the |DFT| related +calculations. This definition is done through the keyword +:option:`density_for_dft density_for_dft`. The density can be: -* WFT : the density is computed with a potentially multi determinant wave function (see variables `psi_det` and `psi_det`)# input_density : the density is set to a density previously stored in the |EZFIO| folder (see ``aux_quantities``) -* damping_rs_dft : the density is damped between the input_density and the WFT density, with a damping factor of :option:`density_for_dft damping_for_rs_dft` +* `WFT`: the density is computed with a potentially multi determinant wave + function (see variables `psi_det` and `psi_det`)# input_density: the density + is set to a density previously stored in the |EZFIO| directory (see + ``aux_quantities``) +* `damping_rs_dft`: the density is damped between the input_density and the WFT + density, with a damping factor of :option:`density_for_dft damping_for_rs_dft` diff --git a/src/determinants/EZFIO.cfg b/src/determinants/EZFIO.cfg index 85c0203d..79cf29eb 100644 --- a/src/determinants/EZFIO.cfg +++ b/src/determinants/EZFIO.cfg @@ -48,12 +48,12 @@ default: 0.99 [n_int] interface: ezfio -doc: Number of integers required to represent bitstrings (set in module :ref:`bitmask`) +doc: Number of integers required to represent bitstrings (set in module :ref:`module_bitmask`) type: N_int_number [bit_kind] interface: ezfio -doc: (set in module :ref:`bitmask`) +doc: (set in module :ref:`module_bitmask`) type: Bit_kind [mo_label] diff --git a/src/determinants/README.rst b/src/determinants/README.rst index 244913b8..df7a2d8e 100644 --- a/src/determinants/README.rst +++ b/src/determinants/README.rst @@ -7,15 +7,15 @@ Contains everything for the computation of the Hamiltonian matrix elements in th The main providers for this module are: * :option:`determinants n_states`: number of states to be computed -* `psi_det`: list of determinants in the wave function used in many routines/providers of the |QP|. -* `psi_coef`: list of coefficients, for all :option:`determinants n_states` states, and all determinants. +* :c:data:`psi_det`: list of determinants in the wave function used in many routines/providers of the |QP|. +* :c:data:`psi_coef`: list of coefficients, for all :option:`determinants n_states` states, and all determinants. The main routines for this module are: -* `i_H_j`: computes the Hamiltonian matrix element between two arbitrary Slater determinants. -* `i_H_j_s2`: computes the Hamiltonian and (:math:`S^2`) matrix element between two arbitrary Slater determinants. -* `i_H_j_verbose`: returns the decomposition in terms of one- and two-body components of the Hamiltonian matrix elements between two arbitrary Slater determinants. Also return the fermionic phase factor. -* `i_H_psi`: computes the Hamiltonian matrix element between an arbitrary Slater determinant and a wave function composed of a sum of arbitrary Slater determinants. +* :c:func:`i_H_j`: computes the Hamiltonian matrix element between two arbitrary Slater determinants. +* :c:func:`i_H_j_s2`: computes the Hamiltonian and (|S^2|) matrix element between two arbitrary Slater determinants. +* :c:func:`i_H_j_verbose`: returns the decomposition in terms of one- and two-body components of the Hamiltonian matrix elements between two arbitrary Slater determinants. Also return the fermionic phase factor. +* :c:func:`i_H_psi`: computes the Hamiltonian matrix element between an arbitrary Slater determinant and a wave function composed of a sum of arbitrary Slater determinants. For an example of how to use these routines and providers, take a look at :file:`example.irp.f`. diff --git a/src/determinants/example.irp.f b/src/determinants/example.irp.f index c8571995..97bc5388 100644 --- a/src/determinants/example.irp.f +++ b/src/determinants/example.irp.f @@ -105,7 +105,7 @@ subroutine example_determinants_psi_det END_DOC read_wf = .True. touch read_wf - ! you force the wave function to be set to the one in the EZFIO folder + ! you force the wave function to be set to the one in the EZFIO directory call routine_example_psi_det end diff --git a/src/dft_utils_in_r/dm_in_r.irp.f b/src/dft_utils_in_r/dm_in_r.irp.f index 777f7ede..8d277453 100644 --- a/src/dft_utils_in_r/dm_in_r.irp.f +++ b/src/dft_utils_in_r/dm_in_r.irp.f @@ -54,13 +54,19 @@ end subroutine density_and_grad_alpha_beta_and_all_aos_and_grad_aos_at_r(r,dm_a,dm_b, grad_dm_a, grad_dm_b, aos_array, grad_aos_array) implicit none BEGIN_DOC -! input : r(1) ==> r(1) = x, r(2) = y, r(3) = z -! output : dm_a = alpha density evaluated at r -! : dm_b = beta density evaluated at r -! : aos_array(i) = ao(i) evaluated at r -! : grad_dm_a(1) = X gradient of the alpha density evaluated in r -! : grad_dm_a(1) = X gradient of the beta density evaluated in r -! : grad_aos_array(1) = X gradient of the aos(i) evaluated at r +! input: +! +! * r(1) ==> r(1) = x, r(2) = y, r(3) = z +! +! output: +! +! * dm_a = alpha density evaluated at r +! * dm_b = beta density evaluated at r +! * aos_array(i) = ao(i) evaluated at r +! * grad_dm_a(1) = X gradient of the alpha density evaluated in r +! * grad_dm_a(1) = X gradient of the beta density evaluated in r +! * grad_aos_array(1) = X gradient of the aos(i) evaluated at r +! END_DOC double precision, intent(in) :: r(3) double precision, intent(out) :: dm_a(N_states),dm_b(N_states) diff --git a/src/fci/README.rst b/src/fci/README.rst index 603d492c..a6a1f962 100644 --- a/src/fci/README.rst +++ b/src/fci/README.rst @@ -9,42 +9,51 @@ fci The user point of view ---------------------- -* :c:func:`fci` performs |CIPSI| calculations using a stochastic scheme for both the selection and the |PT2| contribution, -* :c:func:`pt2` computes the |PT2| contribution using the wave function stored in the |EZFIO| - database. +* :ref:`fci` performs |CIPSI| calculations using a stochastic scheme for both + the selection and the |PT2| contribution, + +* :ref:`pt2` computes the |PT2| contribution using the wave function stored in + the |EZFIO| database. The main keywords/options for this module are: -* :option:`determinants n_det_max` : maximum number of Slater determinants in the CIPSI wave function. The :command:`fci` program will stop when the size of the CIPSI wave function will exceed :option:`determinants n_det_max`. +* :option:`determinants n_det_max` : maximum number of Slater determinants in + the |CIPSI| wave function. The :ref:`fci` program will stop when the size of + the |CIPSI| wave function will exceed :option:`determinants n_det_max`. -* :option:`perturbation pt2_max` : absolute value of the |PT2| to stop the CIPSI calculation. Once the |PT2| :math:`<` :option:`perturbation pt2_max`, the CIPSI calculation stops. +* :option:`perturbation pt2_max` : absolute value of the |PT2| to stop the + |CIPSI| calculation. Once the abs(|PT2|) :math:`<` :option:`perturbation pt2_max`, + the |CIPSI| calculation stops. -* :option:`determinants n_states` : number of states to consider in the CIPSI calculation. +* :option:`determinants n_states` : number of states to consider in the |CIPSI| + calculation. -* :option:`determinants read_wf` : if False, starts with a ROHF-like determinant, if True, starts with the current wave function(s) stored in the |EZFIO| folder. +* :option:`determinants read_wf` : if |false|, starts with a |ROHF|-like + determinant, if |true|, starts with the current wave function(s) stored in + the |EZFIO| directory. .. note:: - For a multi-state calculation, it is recommended to start with :c:func:`cis` or :c:func:`cisd` - wave functions as a guess. + For a multi-state calculation, it is recommended to start with :ref:`cis` + or :ref:`cisd` wave functions as a guess. -* :option:`determinants s2_eig` : if True, systematically add all the determinants needed to have a pure value of :math:`S^2`. Also, if True, it tracks only the states having the good :option:`determinants expected_s2`. +* :option:`determinants expected_s2` : expected value of |S^2| for the + desired spin multiplicity. -.. note:: - For a multi-state calculation, it is recommended to start with :c:func:`cis` or :c:func:`cisd` - wave functions as a guess. - -* :option:`determinants expected_s2` : expected value of :math:`S^2` for the desired spin multiplicity. +* :option:`determinants s2_eig` : if |true|, systematically add all the + determinants needed to have a pure value of |S^2|. Also, if |true|, it + tracks only the states having the good :option:`determinants expected_s2`. -The programmer point of view ----------------------------- -This module have been created with the :ref:`cipsi` module. +The programmer's point of view +------------------------------ + +This module was created with the :ref:`module_cipsi` module. .. seealso:: - The documentation of the :ref:`cipsi` module. + The documentation of the :ref:`module_cipsi` module. diff --git a/src/fci/fci.irp.f b/src/fci/fci.irp.f index 40f683b2..5c747081 100644 --- a/src/fci/fci.irp.f +++ b/src/fci/fci.irp.f @@ -13,7 +13,7 @@ program fci ! conditions: ! ! * number of Slater determinants > :option:`determinants n_det_max` - ! * |PT2| < :option:`perturbation pt2_max` + ! * abs(|PT2|) less than :option:`perturbation pt2_max` ! ! The following other options can be of interest: ! @@ -30,7 +30,7 @@ program fci ! :option:`determinants expected_s2`. ! ! For excited states calculations, it is recommended to start with - ! :ref:`.cis.` or :ref:`.cisd.` guess wave functions, eventually in + ! :ref:`cis` or :ref:`cisd` guess wave functions, eventually in ! a restricted set of |MOs|, and to set :option:`determinants s2_eig` ! to |true|. ! diff --git a/src/fci/pt2.irp.f b/src/fci/pt2.irp.f index 4a555d69..45860fb5 100644 --- a/src/fci/pt2.irp.f +++ b/src/fci/pt2.irp.f @@ -1,13 +1,18 @@ program pt2 implicit none BEGIN_DOC - ! Second order perturbative correction to the wave function contained in the EZFIO directory. + ! Second order perturbative correction to the wave function contained + ! in the |EZFIO| directory. ! - ! This programs runs the stochastic PT2 correction on all "n_states" wave function stored in the EZFIO folder (see :option:`determinant n_states`). + ! This programs runs the stochastic |PT2| correction on all + ! :option:`determinants n_states` wave functions stored in the |EZFIO| + ! directory. ! - ! The option for the PT2 correction are the "pt2_relative_error" which is the relative stochastic + ! The main option for the |PT2| correction is the + ! :option:`perturbation pt2_relative_error` which is the relative + ! stochastic error on the |PT2| to reach before stopping the + ! sampling. ! - ! error on the PT2 to reach before stopping the stochastic sampling. (see :option:`perturbation pt2_relative_error`) END_DOC if (.not. is_zmq_slave) then read_wf = .True. diff --git a/src/hartree_fock/README.rst b/src/hartree_fock/README.rst index 213ae209..38018eb5 100644 --- a/src/hartree_fock/README.rst +++ b/src/hartree_fock/README.rst @@ -8,9 +8,9 @@ calculations (the spatial part of the |MOs| is common for alpha and beta spinorbitals). The Hartree-Fock algorithm is a |SCF| and therefore is based on the -:ref:`module_scf_utils`` module. +:ref:`module_scf_utils` module. -The Fock matrix is defined in :file:`hartree_fock fock_matrix_hf.irp.f`. +The Fock matrix is defined in :file:`fock_matrix_hf.irp.f`. diff --git a/src/mo_basis/mos.irp.f b/src/mo_basis/mos.irp.f index 1380ee09..5547de0c 100644 --- a/src/mo_basis/mos.irp.f +++ b/src/mo_basis/mos.irp.f @@ -236,9 +236,9 @@ subroutine mix_mo_jk(j,k) BEGIN_DOC ! Rotates the j-th |MO| with the k-th |MO| to give two new |MOs| that are ! - ! * $+ = \frac{1}{\sqrt{2}} (|j\rangle + |k\rangle)$ + ! * $+ = \frac{1}{\sqrt{2}} ( | j\rangle + | k\rangle)$ ! - ! * $- = \frac{1}{\sqrt{2}} (|j\rangle - |k\rangle)$ + ! * $- = \frac{1}{\sqrt{2}} ( | j\rangle - | k\rangle)$ ! ! by convention, the '+' |MO| is in the lowest index (min(j,k)) ! by convention, the '-' |MO| is in the highest index (max(j,k)) diff --git a/src/perturbation/perturbation.template.f b/src/perturbation/perturbation.template.f index e9f5f8fd..88c2160a 100644 --- a/src/perturbation/perturbation.template.f +++ b/src/perturbation/perturbation.template.f @@ -6,7 +6,7 @@ END_SHELL subroutine perturb_buffer_$PERT(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) implicit none BEGIN_DOC - ! Applly pertubration ``$PERT`` to the buffer of determinants generated in the H_apply + ! Apply pertubration ``$PERT`` to the buffer of determinants generated in the H_apply ! routine. END_DOC @@ -185,7 +185,7 @@ end subroutine perturb_buffer_by_mono_$PERT(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy) implicit none BEGIN_DOC - ! Applly pertubration ``$PERT`` to the buffer of determinants generated in the H_apply + ! Apply pertubration ``$PERT`` to the buffer of determinants generated in the H_apply ! routine. END_DOC diff --git a/src/perturbation/selection.irp.f b/src/perturbation/selection.irp.f index 2d00f35f..f3f03673 100644 --- a/src/perturbation/selection.irp.f +++ b/src/perturbation/selection.irp.f @@ -1,5 +1,4 @@ -subroutine fill_H_apply_buffer_selection(n_selected,det_buffer,e_2_pert_buffer,coef_pert_buffer, & - N_st,Nint,iproc,select_max_out) +subroutine fill_H_apply_buffer_selection(n_selected,det_buffer,e_2_pert_buffer,coef_pert_buffer, N_st,Nint,iproc,select_max_out) use bitmasks implicit none BEGIN_DOC diff --git a/src/scf_utils/roothaan_hall_scf.irp.f b/src/scf_utils/roothaan_hall_scf.irp.f index c0337d7d..faf23a51 100644 --- a/src/scf_utils/roothaan_hall_scf.irp.f +++ b/src/scf_utils/roothaan_hall_scf.irp.f @@ -174,11 +174,11 @@ END_DOC end -subroutine extrapolate_Fock_matrix( & - error_matrix_DIIS,Fock_matrix_DIIS, & - Fock_matrix_AO_,size_Fock_matrix_AO, & - iteration_SCF,dim_DIIS & -) +subroutine extrapolate_Fock_matrix( & + error_matrix_DIIS,Fock_matrix_DIIS, & + Fock_matrix_AO_,size_Fock_matrix_AO, & + iteration_SCF,dim_DIIS & + ) BEGIN_DOC ! Compute the extrapolated Fock matrix using the DIIS procedure diff --git a/src/selectors_cassd/README.rst b/src/selectors_cassd/README.rst index e359ef8e..d4a648d3 100644 --- a/src/selectors_cassd/README.rst +++ b/src/selectors_cassd/README.rst @@ -3,4 +3,4 @@ selectors_cassd =============== Selectors for |CAS-SD| calculations. The selectors are defined as first the -generators from :ref:`Generators_CAS`, and then the rest of the wave function. +generators from :ref:`module_generators_cas`, and then the rest of the wave function. diff --git a/src/tools/diagonalize_h.irp.f b/src/tools/diagonalize_h.irp.f index 5b3cbdf5..c9ae2033 100644 --- a/src/tools/diagonalize_h.irp.f +++ b/src/tools/diagonalize_h.irp.f @@ -1,11 +1,14 @@ program diagonalize_h implicit none BEGIN_DOC -! Program that extracts the :option:`determinants n_states` lowest states of the Hamiltonian within the set of Slater determinants stored in the EZFIO folder. +! Program that extracts the :option:`determinants n_states` lowest +! states of the Hamiltonian within the set of Slater determinants stored +! in the |EZFIO| directory. ! -! If :option:`determinants s2_eig` = True, it will retain only states +! If :option:`determinants s2_eig` = |true|, it will retain only states +! which correspond to the desired value of +! :option:`determinants expected_s2`. ! -! which corresponds to the desired value of :option:`determinants expected_s2`. END_DOC read_wf = .True. touch read_wf diff --git a/src/tools/fcidump.irp.f b/src/tools/fcidump.irp.f index f979ac1a..bf4d07fb 100644 --- a/src/tools/fcidump.irp.f +++ b/src/tools/fcidump.irp.f @@ -1,17 +1,22 @@ program fcidump implicit none BEGIN_DOC -! Produce a regular FCIDUMP file from the |MOs| stored in the |EZFIO| folder. +! Produce a regular `FCIDUMP` file from the |MOs| stored in the |EZFIO| +! directory. ! -! To specify an active space, the class of the mos have to set in the |EZFIO| folder (see :ref:`qp_set_mo_class`). +! To specify an active space, the class of the |MOs| have to set in the +! |EZFIO| directory (see :ref:`qp_set_mo_class`). ! -! The fcidump program supports 3 types of MO_class : +! The :ref:`fcidump` program supports 3 types of |MO| classes : ! -! * the "core" orbitals which are always doubly occupied in the calculation +! * the *core* orbitals which are always doubly occupied in the +! calculation ! -! * the "del" orbitals that are never occupied in the calculation +! * the *deleted* orbitals that are never occupied in the calculation +! +! * the *active* orbitals that are occupied with a varying number of +! electrons ! -! * the "act" orbitals that will be occupied by a varying number of electrons END_DOC character*(128) :: output integer :: i_unit_output,getUnitAndOpen diff --git a/src/tools/four_idx_transform.irp.f b/src/tools/four_idx_transform.irp.f index 45198770..92e87cad 100644 --- a/src/tools/four_idx_transform.irp.f +++ b/src/tools/four_idx_transform.irp.f @@ -1,11 +1,15 @@ program four_idx_transform implicit none BEGIN_DOC -! 4-index transformation of two-electron integrals from |AO| to |MO| integrals. +! 4-index transformation of two-electron integrals from |AO| to |MO| +! integrals. ! -! This program will compute the two-electron integrals on the |MO| basis and store it into the |EZFIO| folder. +! This program will compute the two-electron integrals on the |MO| basis +! and store it into the |EZFIO| directory. +! +! This program can be useful if the AO --> MO transformation is an +! expensive step by itself. ! -! This program can be useful if the AO --> MO transformation is an expensive step by itself. END_DOC io_mo_two_e_integrals = 'Write' diff --git a/src/tools/molden.irp.f b/src/tools/molden.irp.f index f22592f6..081e74db 100644 --- a/src/tools/molden.irp.f +++ b/src/tools/molden.irp.f @@ -1,7 +1,7 @@ program molden implicit none BEGIN_DOC - ! Produce a Molden file + ! Produces a Molden file END_DOC character*(128) :: output integer :: i_unit_output,getUnitAndOpen diff --git a/src/tools/print_wf.irp.f b/src/tools/print_wf.irp.f index 2a8335fc..01fc8948 100644 --- a/src/tools/print_wf.irp.f +++ b/src/tools/print_wf.irp.f @@ -1,17 +1,20 @@ program print_wf implicit none BEGIN_DOC - ! Print the ground state wave function stored in the |EZFIO| folder in the intermediate normalization. + ! Print the ground state wave function stored in the |EZFIO| directory + ! in the intermediate normalization. ! - ! It also prints a lot of information regarding the excitation operators from the reference determinant + ! It also prints a lot of information regarding the excitation + ! operators from the reference determinant ! and a first-order + ! perturbative analysis of the wave function. ! - ! and a first-order perturbative analysis of the wave function. - ! - ! If the wave function strongly deviates from the first-order analysis, something funny is going on :) + ! If the wave function strongly deviates from the first-order analysis, + ! something funny is going on :) END_DOC - ! this has to be done in order to be sure that N_det, psi_det and psi_coef are the wave function stored in the EZFIO folder + ! this has to be done in order to be sure that N_det, psi_det and + ! psi_coef are the wave function stored in the |EZFIO| directory. read_wf = .True. touch read_wf call routine diff --git a/src/tools/save_natorb.irp.f b/src/tools/save_natorb.irp.f index e18309ba..88b28f06 100644 --- a/src/tools/save_natorb.irp.f +++ b/src/tools/save_natorb.irp.f @@ -1,15 +1,16 @@ program save_natorb implicit none BEGIN_DOC -! Save natural MOs into the EZFIO +! Save natural |MOs| into the |EZFIO|. ! -! This program reads the wave function stored in the EZFIO folder, +! This program reads the wave function stored in the |EZFIO| directory, +! extracts the corresponding natural orbitals and setd them as the new +! |MOs|. ! -! extracts the corresponding natural orbitals and set them as the new MOs -! -! If this is a multi-state calculation, the density matrix that produces the natural orbitals -! -! is obtained from a state-averaged of the density matrices of each state with the corresponding state_average_weight (see the doc of state_average_weight). +! If this is a multi-state calculation, the density matrix that produces +! the natural orbitals is obtained from an average of the density +! matrices of each state with the corresponding +! :option:`determinants state_average_weight` END_DOC read_wf = .True. touch read_wf diff --git a/src/tools/save_one_e_dm.irp.f b/src/tools/save_one_e_dm.irp.f index 9bfa6717..e850131e 100644 --- a/src/tools/save_one_e_dm.irp.f +++ b/src/tools/save_one_e_dm.irp.f @@ -1,13 +1,16 @@ program save_one_e_dm implicit none BEGIN_DOC -! programs that computes the one body density on the mo basis for alpha and beta electrons - -! from the wave function stored in the EZFIO folder, and then save it into the EZFIO folder aux_quantities. +! Program that computes the one body density on the |MO| basis +! for $\alpha$ and $\beta$ electrons from the wave function +! stored in the |EZFIO| directory, and then saves it into the +! :ref:`module_aux_quantities`. ! -! Then, the global variable data_one_e_dm_alpha_mo and data_one_e_dm_beta_mo will automatically read this density in a further calculation. -! -! This can be used to perform damping on the density in RS-DFT calculation (see the density_for_dft module). +! Then, the global variable :option:`aux_quantities data_one_e_dm_alpha_mo` +! and :option:`aux_quantities data_one_e_dm_beta_mo` will automatically +! read this density in the next calculation. This can be used to perform +! damping on the density in |RSDFT| calculations (see +! :ref:`module_density_for_dft`). END_DOC read_wf = .True. touch read_wf diff --git a/src/tools/write_integrals_erf.irp.f b/src/tools/write_integrals_erf.irp.f index b527576d..89c818f6 100644 --- a/src/tools/write_integrals_erf.irp.f +++ b/src/tools/write_integrals_erf.irp.f @@ -1,7 +1,8 @@ program write_integrals_erf implicit none BEGIN_DOC - ! Saves the two-electron integrals with the :math:`erf(\mu r_{12})/r_{12}` oprerator into the EZFIO folder + ! Saves the two-electron integrals with the $erf(\mu r_{12})/r_{12}$ + ! oprerator into the EZFIO directory. END_DOC io_mo_two_e_integrals = 'None' touch io_mo_two_e_integrals