mirror of
https://github.com/LCPQ/quantum_package
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Merge pull request #13 from scemama/master
Qp_create working with pseudo
This commit is contained in:
Thomas Applencourt
commit
763e77444d
@ -13,8 +13,8 @@ let spec =
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~doc:"int Total charge of the molecule. Default is 0."
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+> flag "m" (optional_with_default 1 int)
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~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
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+> flag "p" (optional_with_default 0 int)
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~doc:"Using pseudo. Default is not (aka 0)"
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+> flag "p" no_arg
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~doc:"Using pseudo."
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+> anon ("xyz_file" %: string)
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;;
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@ -62,12 +62,12 @@ let run ?o b c m p xyz_file =
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| None -> (* Principal basis *)
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let basis = elem_and_basis_name in
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let command =
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if (p = 0) then
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Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
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^ "\" \"" ^ basis ^"\""
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else
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if (p) then
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Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
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^ "\" \"" ^ basis ^"\" pseudo"
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else
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Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
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^ "\" \"" ^ basis ^"\""
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in
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begin
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let filename =
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@ -254,7 +254,11 @@ let run ?o b c m p xyz_file =
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(* Doesn't work... *)
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(* if p = 1 then Qpackage.root ^ "scripts/pseudo/put_pseudo_in_ezfio.py" ezfio_file.to_string; *)
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if (p) then
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begin
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Qpackage.root ^ "/scripts/pseudo/put_pseudo_in_ezfio.py " ^ ezfio_file
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|> Sys.command_exn
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end;
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match Input.Ao_basis.read () with
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| None -> failwith "Error in basis"
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@ -16,6 +16,7 @@ fi
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cd ${QPACKAGE_ROOT}
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rm -rf resultsFile-master
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${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/resultsFile.tar.gz
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tar -zxf resultsFile.tar.gz && rm resultsFile.tar.gz ||exit 1
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mv resultsFile-master resultsFile
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@ -12,15 +12,15 @@ QPACKAGE_ROOT="$( cd "$(dirname "$BASH_SOURCE")" ; pwd -P )"
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cat << EOF > quantum_package.rc
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export IRPF90="${IRPF90}"
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export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P )
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export IRPF90="\${QPACKAGE_ROOT}/bin/irpf90"
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export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
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export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
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export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH}
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export PYTHONPATH=\${PYTHONPATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
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export PYTHONPATH=\${PYTHONPATH}\$(find "\${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
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export PATH=\${PATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
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export PATH=\${PATH}\$(find "\${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
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export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
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export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
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source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
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@ -30,6 +30,8 @@ Assumptions
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.. Do not edit this section. It was auto-generated from the
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.. NEEDED_MODULES file.
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* The AO coefficients in the EZFIO files are not necessarily normalized and are normalized after reading
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Needed Modules
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==============
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@ -29,7 +29,7 @@ Documentation
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integral of the AO basis <ik|jl> or (ij|kl)
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i(r1) j(r1) 1/r12 k(r2) l(r2)
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`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L490>`_
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`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L491>`_
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Needed to compute Schwartz inequalities
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`ao_bielec_integral_schwartz_accel <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L107>`_
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@ -46,48 +46,48 @@ Documentation
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`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L290>`_
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Compute AO 1/r12 integrals for all i and fixed j,k,l
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`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L653>`_
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`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L654>`_
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ATOMIC PRIMTIVE bielectronic integral between the 4 primitives ::
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primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
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primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2)
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primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
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primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)
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`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L515>`_
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`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L516>`_
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Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
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`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L851>`_
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`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L852>`_
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subroutine that returns the explicit polynom in term of the "t"
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variable of the following polynomw :
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I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
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`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L772>`_
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`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L773>`_
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recursive function involved in the bielectronic integral
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`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L914>`_
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`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L915>`_
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recursive function involved in the bielectronic integral
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`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1034>`_
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`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1035>`_
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recursive function involved in the bielectronic integral
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`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1088>`_
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`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1089>`_
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recursive function involved in the bielectronic integral
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`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L948>`_
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`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L949>`_
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recursive function involved in the bielectronic integral
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`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L807>`_
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`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L808>`_
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recursive function involved in the bielectronic integral
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`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1150>`_
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`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1151>`_
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recursive function involved in the bielectronic integral
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`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L698>`_
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`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L699>`_
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calculate the integral of the polynom ::
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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)
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between ( 0 ; 1)
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`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L837>`_
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`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L838>`_
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Returns the upper boundary of the degree of the polynomial involved in the
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bielctronic integral :
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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)
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@ -165,32 +165,32 @@ Documentation
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`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L42>`_
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Adds integrals to tha MO map according to some bitmask
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`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L464>`_
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`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L465>`_
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mo_bielec_integral_jj(i,j) = J_ij
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mo_bielec_integral_jj_exchange(i,j) = K_ij
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mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
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`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L466>`_
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`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L467>`_
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mo_bielec_integral_jj(i,j) = J_ij
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mo_bielec_integral_jj_exchange(i,j) = K_ij
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mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
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`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L326>`_
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`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L327>`_
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mo_bielec_integral_jj_from_ao(i,j) = J_ij
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mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
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mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
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`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L465>`_
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`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L466>`_
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mo_bielec_integral_jj(i,j) = J_ij
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mo_bielec_integral_jj_exchange(i,j) = K_ij
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mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
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`mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L325>`_
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`mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L326>`_
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mo_bielec_integral_jj_from_ao(i,j) = J_ij
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mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
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mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
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`mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L324>`_
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`mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L325>`_
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mo_bielec_integral_jj_from_ao(i,j) = J_ij
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mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
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mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
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@ -481,6 +481,7 @@ IRP_ENDIF COARRAY
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ao_bielec_integrals_in_map = .True.
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if (write_ao_integrals) then
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call dump_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin')
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call ezfio_set_bielec_integrals_disk_access_ao_integrals(.True.)
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endif
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END_PROVIDER
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@ -312,6 +312,7 @@ IRP_ENDIF
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if (write_mo_integrals) then
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call dump_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin')
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call ezfio_set_bielec_integrals_disk_access_mo_integrals(.True.)
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endif
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@ -45,10 +45,10 @@ Documentation
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after calling this function.
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After calling this subroutine, N_det, psi_det and psi_coef need to be touched
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`debug_unicity_of_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L187>`_
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`debug_unicity_of_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L187>`_
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This subroutine checks that there are no repetitions in the wave function
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`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L222>`_
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`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L222>`_
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Fill the H_apply buffer with determiants for CISD
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`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L15>`_
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@ -329,7 +329,7 @@ Documentation
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`ci_sc2_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L1>`_
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N_states_diag lowest eigenvalues of the CI matrix
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`diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L46>`_
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`diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L45>`_
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Replace the coefficients of the CI states_diag by the coefficients of the
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eigenstates of the CI matrix
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@ -337,52 +337,52 @@ subroutine write_spindeterminants
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call ezfio_set_spindeterminants_psi_coef_matrix_rows(psi_svd_matrix_rows)
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call ezfio_set_spindeterminants_psi_coef_matrix_columns(psi_svd_matrix_columns)
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integer :: n_svd_coefs
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double precision :: norm, f
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f = 1.d0/dble(N_states)
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norm = 1.d0
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do n_svd_coefs=1,N_det_alpha_unique
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do k=1,N_states
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norm -= psi_svd_coefs(n_svd_coefs,k)*psi_svd_coefs(n_svd_coefs,k)
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enddo
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if (norm < 1.d-4) then
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exit
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endif
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enddo
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n_svd_coefs -= 1
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call ezfio_set_spindeterminants_n_svd_coefs(n_svd_coefs)
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double precision, allocatable :: dtmp(:,:,:)
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allocate(dtmp(N_det_alpha_unique,n_svd_coefs,N_states))
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do k=1,N_states
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do j=1,n_svd_coefs
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do i=1,N_det_alpha_unique
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dtmp(i,j,k) = psi_svd_alpha(i,j,k)
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enddo
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enddo
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enddo
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call ezfio_set_spindeterminants_psi_svd_alpha(dtmp)
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deallocate(dtmp)
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allocate(dtmp(N_det_beta_unique,n_svd_coefs,N_states))
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do k=1,N_states
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do j=1,n_svd_coefs
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do i=1,N_det_beta_unique
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dtmp(i,j,k) = psi_svd_beta(i,j,k)
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enddo
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enddo
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enddo
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call ezfio_set_spindeterminants_psi_svd_beta(dtmp)
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deallocate(dtmp)
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allocate(dtmp(n_svd_coefs,N_states,1))
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do k=1,N_states
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do j=1,n_svd_coefs
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dtmp(j,k,1) = psi_svd_coefs(j,k)
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enddo
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enddo
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call ezfio_set_spindeterminants_psi_svd_coefs(dtmp)
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deallocate(dtmp)
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! integer :: n_svd_coefs
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! double precision :: norm, f
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! f = 1.d0/dble(N_states)
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! norm = 1.d0
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! do n_svd_coefs=1,N_det_alpha_unique
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! do k=1,N_states
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! norm -= psi_svd_coefs(n_svd_coefs,k)*psi_svd_coefs(n_svd_coefs,k)
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! enddo
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! if (norm < 1.d-4) then
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! exit
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! endif
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! enddo
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! n_svd_coefs -= 1
|
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! call ezfio_set_spindeterminants_n_svd_coefs(n_svd_coefs)
|
||||
!
|
||||
! double precision, allocatable :: dtmp(:,:,:)
|
||||
! allocate(dtmp(N_det_alpha_unique,n_svd_coefs,N_states))
|
||||
! do k=1,N_states
|
||||
! do j=1,n_svd_coefs
|
||||
! do i=1,N_det_alpha_unique
|
||||
! dtmp(i,j,k) = psi_svd_alpha(i,j,k)
|
||||
! enddo
|
||||
! enddo
|
||||
! enddo
|
||||
! call ezfio_set_spindeterminants_psi_svd_alpha(dtmp)
|
||||
! deallocate(dtmp)
|
||||
!
|
||||
! allocate(dtmp(N_det_beta_unique,n_svd_coefs,N_states))
|
||||
! do k=1,N_states
|
||||
! do j=1,n_svd_coefs
|
||||
! do i=1,N_det_beta_unique
|
||||
! dtmp(i,j,k) = psi_svd_beta(i,j,k)
|
||||
! enddo
|
||||
! enddo
|
||||
! enddo
|
||||
! call ezfio_set_spindeterminants_psi_svd_beta(dtmp)
|
||||
! deallocate(dtmp)
|
||||
!
|
||||
! allocate(dtmp(n_svd_coefs,N_states,1))
|
||||
! do k=1,N_states
|
||||
! do j=1,n_svd_coefs
|
||||
! dtmp(j,k,1) = psi_svd_coefs(j,k)
|
||||
! enddo
|
||||
! enddo
|
||||
! call ezfio_set_spindeterminants_psi_svd_coefs(dtmp)
|
||||
! deallocate(dtmp)
|
||||
|
||||
end
|
||||
|
||||
|
||||
@ -10,9 +10,6 @@ Documentation
|
||||
.. Do not edit this section. It was auto-generated from the
|
||||
.. NEEDED_MODULES file.
|
||||
|
||||
`fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/FCIdump/fcidump.irp.f#L1>`_
|
||||
Undocumented
|
||||
|
||||
|
||||
|
||||
Needed Modules
|
||||
|
||||
@ -18,6 +18,18 @@ When saving the MOs, the ``mo_basis`` directory of the EZFIO file is copied
|
||||
in the ``save`` directory, named by the current ``mo_label``. All this is
|
||||
done with the script named ``save_current_mos.sh`` in the ``scripts`` directory.
|
||||
|
||||
Assumptions
|
||||
===========
|
||||
|
||||
.. Do not edit this section. It was auto-generated from the
|
||||
.. NEEDED_MODULES file.
|
||||
|
||||
ASSUMPTONS
|
||||
==========
|
||||
|
||||
* The AO basis functions are normalized.
|
||||
|
||||
|
||||
Needed Modules
|
||||
==============
|
||||
|
||||
|
||||
@ -17,7 +17,7 @@ from collections import defaultdict
|
||||
# O p t #
|
||||
# ~#~#~ #
|
||||
|
||||
precision = 5.e-8
|
||||
precision = 1.e-7
|
||||
|
||||
# A test get a geo file and a basis file.
|
||||
# A global dict containt the result for this test
|
||||
|
||||
Loading…
Reference in New Issue
Block a user