added direct, exchange between extra_basis and usual basis, together with a tuto in ao_extra_basis

plugins/local/extra_basis_int/ao_overlap.irp.f

@@ -4,7 +4,7 @@
  BEGIN_PROVIDER [double precision, ao_extra_overlap  , (ao_extra_num, ao_extra_num)]
 
   BEGIN_DOC
-  ! Overlap between atomic basis functions:
+  ! Overlap between atomic basis functions belonging to the EXTRA BASIS 
   !
   ! :math:`\int \chi_i(r) \chi_j(r) dr`
   END_DOC
@@ -71,6 +71,8 @@ END_PROVIDER
   BEGIN_DOC
   ! Overlap between atomic basis functions:  
   !
+  ! first index belongs to the REGULAR AO basis, second to the EXTRA basis 
+  !
   ! <AO_i|AO_j extra basis>
   END_DOC
 

plugins/local/extra_basis_int/pot_ao_ints.irp.f

@@ -5,7 +5,6 @@ BEGIN_PROVIDER [ double precision, pot_vne_A_extra_basis, (ao_extra_num,ao_extra
   ! Computes the following integral :
   ! $\sum_{R in the USUAL nuclei} -Z <chi_i|1/|r-R||chi_j>$ 
   !
-  !
   ! where $\chi_i(r)$ AND $\chi_j(r)$ belongs to the EXTRA basis 
   END_DOC
   integer :: mu,nu

plugins/local/extra_basis_int/v_mixed_extra.irp.f

@@ -9,9 +9,9 @@ double precision function v_extra_nucl_extra_ao(i_ao,j_ao)
   ! $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) v_ne^{extra}(r)$.
   !
   !
-  ! where BOTH $\chi_i(r)$ AND $\chi_j(r)$ belongs to the EXTRA basis 
+  ! where BOTH $\chi_i(r)$ AND $\chi_j(r)$ belongs to the EXTRA basis (system B)
   !
-  ! and v_ne^{extra}(r) is the Coulomb potential coming from the EXTRA nuclei
+  ! and v_ne^{extra}(r) is the Coulomb potential coming from the EXTRA nuclei (system B)
   END_DOC
  integer, intent(in) ::i_ao,j_ao
  double precision :: mu_in,charge,coord(3)
@@ -34,9 +34,9 @@ double precision function v_extra_nucl_ao(i_ao,j_ao)
   ! $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) v_ne(r)$.
   !
   !
-  ! where BOTH $\chi_i(r)$ AND $\chi_j(r)$ belongs to the REGULAR basis 
+  ! where BOTH $\chi_i(r)$ AND $\chi_j(r)$ belongs to the REGULAR basis (system A)
   !
-  ! and v_ne(r) is the Coulomb potential coming from the EXTRA nuclei
+  ! and v_ne(r) is the Coulomb potential coming from the EXTRA nuclei (system B)
   END_DOC
  integer, intent(in) ::i_ao,j_ao
  integer :: i
@@ -59,9 +59,9 @@ double precision function v_nucl_extra_ao(i_ao,j_ao)
   ! $\int_{-\infty}^{infty} dr \chi_i(r) \chi_j(r) v_ne(r)$.
   !
   !
-  ! where BOTH $\chi_i(r)$ AND $\chi_j(r)$ belongs to the EXTRA basis 
+  ! where BOTH $\chi_i(r)$ AND $\chi_j(r)$ belongs to the EXTRA basis (system B)
   !
-  ! and v_ne(r) is the Coulomb potential coming from the REGULAR nuclei
+  ! and v_ne(r) is the Coulomb potential coming from the REGULAR nuclei (system A)
   END_DOC
  integer, intent(in) ::i_ao,j_ao
  double precision :: mu_in,charge,coord(3)

src/ao_extra_basis/README.rst

@@ -5,7 +5,9 @@ extra_basis
 Plugin to handle an extra basis, which is attached to the extra_nuclei.
 It is essentially a duplication of all important quantities (coefficients, exponents and so on) of the usual |AO| basis. 
 
-An interesting feature is the possibility to fit any basis made at most with "p" functions onto a purely "s" basis. 
+Check in the directory "tuto" for a simple example of how to create a fictious system "B" attached independently to a system "A"
+
+Another interesting feature is the possibility to fit any basis made at most with "p" functions onto a purely "s" basis. 
 This is done with the various scripts here: 
  
  - qp_fit_1s_basis : script that creates an |EZFIO| folder corresponding to an .xyz file and a basis fitted with only "s" functions
@@ -13,3 +15,4 @@ This is done with the various scripts here:
  
 Ex: 
 qp_add_extra_fit_system LiH.ezfio/ h2o.xyz # takes the EZFIO folder "LiH.ezfio" and creates all necessary additional basis and nuclei based on h2o.xyz, but only with 1s functions. 
+

src/ao_extra_basis/tuto/He_A.xyz

@@ -0,0 +1,3 @@
+1
+He atom "A"
+He 0. 0. 0.

src/ao_extra_basis/tuto/example_copy.sh

@@ -0,0 +1,26 @@
+source ~/qp2/quantum_package.rc
+## Example of how to generate an additional h2o molecule, stored as a extra basis/nuclei etc .. to an He
+
+sys_B=h2o.xyz
+basis_B=sto-3g
+output_B=${sys_B%.xyz}_${basis_B}
+
+sys_A=He_A.xyz
+basis_A=cc-pvtz
+output_A=${sys_A%.xyz}_${basis_A}_extra_${output_B}
+
+# we create the system "B" that will be attached as an "extra system" to the syste "A"
+qp create_ezfio -b $basis_B $sys_B -o ${output_B}
+# we perform an HF calculation to obtain the AO density matrix 
+qp run scf 
+# we save the density matrix in the EZFIO
+qp run save_one_e_dm 
+# we create the system "A" 
+qp create_ezfio -b $basis_A $sys_A -o ${output_A}
+# We perform an SCF calculation
+qp run scf 
+# we copy the system "B" information as extra nuclei/basis etc in the EZFIO of system "A"
+qp_copy_extra_basis ${output_B} ${output_A}
+
+# we execute an example of progra that prints a lot of useful integrals/information on the A-B interaction
+qp run test_extra_basis | tee ${output_A}.test_extra_basis

src/ao_extra_basis/tuto/h2o.xyz

@@ -0,0 +1,7 @@
+3
+
+O      0.000000    -0.399441  3.000000   
+H      0.761232     0.199721  3.000000   
+H     -0.761232     0.199721  3.000000   
+
+