Merge pull request #66 from scemama/master

Updated Pseudopotential and IRPF90/Ninja build

Author: scemama

scripts/get_basis.sh

@@ -51,5 +51,7 @@ then
     ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}"
 else
     ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db"
+#    echo ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db" 1>&2
+#    echo $PWD/BASIS
 fi
 

scripts/fetch_from_web.py renamed to scripts/install/fetch_from_web.py

@@ -22,7 +22,7 @@ then
 fi
 
 rm -f -- ${QPACKAGE_ROOT}/bin/curl
-${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${CURL_URL} CURL.tar.bz2
+${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${CURL_URL} CURL.tar.bz2
 tar -jxf CURL.tar.bz2 && rm CURL.tar.bz2 ||exit 1
 cd ${CURL} || exit 1 
 mv curl.ermine ${QPACKAGE_ROOT}/bin/curl

scripts/install/install_curl.sh

@@ -16,6 +16,6 @@ fi
 cd ${QPACKAGE_ROOT}
 
 rm -f -- scripts/${DOCOPT}{,c}
-${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${DOCOPT_URL} ${DOCOPT}
+${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${DOCOPT_URL} ${DOCOPT}
 
-mv ${DOCOPT} scripts/${DOCOPT}
+mv ${DOCOPT} scripts/${DOCOPT}

scripts/install/install_docopt.sh

@@ -15,7 +15,7 @@ fi
 
 cd ${QPACKAGE_ROOT}
 
-${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
+${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
 tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
 rm -rf EMSL_Basis
 mv ${BASE}-master EMSL_Basis

scripts/install/install_emsl.sh

@@ -16,7 +16,7 @@ fi
 cd ${QPACKAGE_ROOT}
 
 rm -rf -- EZFIO
-${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
+${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
 tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
 mv EZFIO-master EZFIO
 

scripts/install/install_ezfio.sh

@@ -17,7 +17,7 @@ fi
 cd ${QPACKAGE_ROOT}
 
 
-${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
+${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
 tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
 mv ${BASE}-master irpf90
 make -C irpf90 | tee install_irpf90.log

scripts/install/install_irpf90.sh

@@ -20,7 +20,7 @@ rm -f l${QPACKAGE_ROOT}/bin/m4
 if [[ -z ${M4} ]] 
 then 
     rm -f -- bin/m4
-    ${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${M4_URL} M4.tar.gz 
+    ${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${M4_URL} M4.tar.gz 
     tar -zxf M4.tar.gz && rm M4.tar.gz ||exit 1
     cd m4* || exit 1 
     ./configure && make || exit 1 

scripts/install/install_m4.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#
+# Installs the ninja build system
+# Thu May 28 13:21:16 CEST 2015
+
+BASE="ninja"
+URL="https://github.com/martine/ninja/archive/master.tar.gz"
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  echo "The QPACKAGE_ROOT environment variable is not set."
+  echo "Please reload the quantum_package.rc file."
+  exit -1
+fi
+cd ${QPACKAGE_ROOT}
+${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
+tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
+rm -rf ${BASE}
+mv ${BASE}-master ${BASE}
+cd ${BASE}
+./configure.py --bootstrap
+

scripts/install/install_ninja.sh

@@ -45,7 +45,7 @@ then
     done
   fi
 fi
-${QPACKAGE_ROOT}/scripts/fetch_from_web.py \
+${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py \
    "https://raw.github.com/ocaml/opam/master/shell/opam_installer.sh" opam_installer.sh
 chmod +x opam_installer.sh
 echo N | ./opam_installer.sh ${QPACKAGE_ROOT}/bin 

scripts/install/install_ocaml.sh

@@ -23,12 +23,12 @@ DEPS="$NEEDED_MODULES"
 for M in ${DEPS}
 do
   # X is the list of external source files
-  X=$(grep 'SRC=' "${QPACKAGE_ROOT}/src/${M}/Makefile" 2>/dev/null |cut -d '=' -f 2) 
+  X=$(grep '^SRC=' "${QPACKAGE_ROOT}/src/${M}/Makefile" 2>/dev/null |cut -d '=' -f 2) 
   for f in ${X}
   do
     SRC+=" ${M}/${f}"
   done
-  X=$(grep 'OBJ=' "${QPACKAGE_ROOT}/src/${M}/Makefile" 2>/dev/null |cut -d '=' -f 2) 
+  X=$(grep '^OBJ=' "${QPACKAGE_ROOT}/src/${M}/Makefile" 2>/dev/null |cut -d '=' -f 2) 
   for f in ${X}
   do
     OBJ+=" IRPF90_temp/${M}/${f/IRPF90_temp//}"

scripts/module/create_Makefile_depend.sh

@@ -3,7 +3,7 @@
  implicit none
  integer :: n_pt_sup
  integer :: prim_power_l_max
- include 'constants.F'
+ include 'include/constants.F'
  prim_power_l_max = maxval(ao_power)
  n_pt_max_integrals = 24 * prim_power_l_max + 4
  n_pt_max_i_x = 8 * prim_power_l_max

src/AOs/dimensions_integrals.irp.f

@@ -1,6 +1,7 @@
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
-SRC=H_apply_template.f
+#SRC=H_apply_template.f
+SRC=
 OBJ=
 
 include $(QPACKAGE_ROOT)/src/Makefile.common

src/Determinants/Makefile

@@ -519,7 +519,7 @@ double precision function general_primitive_integral(dim,            &
   ! Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
   END_DOC
   integer,intent(in)             :: dim
-  include 'constants.F'
+  include 'include/constants.F'
   double precision, intent(in)   :: P_new(0:max_dim,3),P_center(3),fact_p,p,p_inv
   double precision, intent(in)   :: Q_new(0:max_dim,3),Q_center(3),fact_q,q,q_inv
   integer, intent(in)            :: iorder_p(3)
@@ -665,7 +665,7 @@ double precision function ERI(alpha,beta,delta,gama,a_x,b_x,c_x,d_x,a_y,b_y,c_y,
   integer                        :: n_pt_sup
   double precision               :: p,q,denom,coeff
   double precision               :: I_f
-  include 'constants.F'
+  include 'include/constants.F'
   if(iand(a_x+b_x+c_x+d_x,1).eq.1.or.iand(a_y+b_y+c_y+d_y,1).eq.1.or.iand(a_z+b_z+c_z+d_z,1).eq.1)then
     ERI = 0.d0
     return
@@ -859,7 +859,7 @@ subroutine give_polynom_mult_center_x(P_center,Q_center,a_x,d_x,p,q,n_pt_in,pq_i
   integer, intent(in)            :: a_x,d_x
   double precision, intent(in)   :: P_center, Q_center
   double precision, intent(in)   :: p,q,pq_inv,p10_1,p01_1,p10_2,p01_2,pq_inv_2
-  include 'constants.F'
+  include 'include/constants.F'
   double precision,intent(out)   :: d(0:max_dim)
   double precision               :: accu
   accu = 0.d0
@@ -916,7 +916,7 @@ 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 bielectronic integral
   END_DOC
   integer , intent(in)           :: n_pt_in
-  include 'constants.F'
+  include 'include/constants.F'
   double precision,intent(inout) :: d(0:max_dim)
   integer,intent(inout)          :: nd
   integer, intent(in)            :: a,c
@@ -950,7 +950,7 @@ recursive subroutine I_x1_pol_mult_recurs(a,c,B_10,B_01,B_00,C_00,D_00,d,nd,n_pt
   ! recursive function involved in the bielectronic integral
   END_DOC
   integer , intent(in)           :: n_pt_in
-  include 'constants.F'
+  include 'include/constants.F'
   double precision,intent(inout) :: d(0:max_dim)
   integer,intent(inout)          :: nd
   integer, intent(in)            :: a,c
@@ -1036,7 +1036,7 @@ 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 bielectronic integral
   END_DOC
   integer , intent(in)           :: n_pt_in
-  include 'constants.F'
+  include 'include/constants.F'
   double precision,intent(inout) :: d(0:max_dim)
   integer,intent(inout)          :: nd
   integer, intent(in)            :: c
@@ -1090,7 +1090,7 @@ 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 bielectronic integral
   END_DOC
   integer , intent(in)           :: n_pt_in
-  include 'constants.F'
+  include 'include/constants.F'
   double precision,intent(inout) :: d(0:max_dim)
   integer,intent(inout)          :: nd
   integer, intent(in)            :: c
@@ -1152,7 +1152,7 @@ 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 bielectronic integral
   END_DOC
   integer , intent(in)           :: dim
-  include 'constants.F'
+  include 'include/constants.F'
   double precision               :: d(0:max_dim)
   integer,intent(inout)          :: nd
   integer, intent(in)            :: c

src/Integrals_Bielec/ao_bi_integrals.irp.f

@@ -148,7 +148,7 @@ double precision function NAI_pol_mult(A_center,B_center,power_A,power_B,alpha,b
 double precision :: d(0:n_pt_in),pouet,coeff,rho,dist,const,pouet_2,p,p_inv,factor
 double precision :: I_n_special_exact,integrate_bourrin,I_n_bibi
 double precision ::  V_e_n,const_factor,dist_integral,tmp
-include 'constants.F'
+include 'include/constants.F'
   if ( (A_center(1)/=B_center(1)).or. &
        (A_center(2)/=B_center(2)).or. &
        (A_center(3)/=B_center(3)).or. &
@@ -351,7 +351,7 @@ recursive subroutine I_x1_pol_mult_mono_elec(a,c,R1x,R1xp,R2x,d,nd,n_pt_in)
  integer,intent(inout) :: nd
  integer, intent(in):: a,c
  double precision, intent(in) :: R1x(0:2),R1xp(0:2),R2x(0:2)
- include 'constants.F'
+ include 'include/constants.F'
   double precision :: X(0:max_dim)
   double precision :: Y(0:max_dim)
   !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: X, Y
@@ -417,7 +417,7 @@ recursive subroutine I_x1_pol_mult_mono_elec(a,c,R1x,R1xp,R2x,d,nd,n_pt_in)
 recursive subroutine I_x2_pol_mult_mono_elec(c,R1x,R1xp,R2x,d,nd,dim) 
  implicit none
  integer , intent(in) :: dim
- include 'constants.F'
+ include 'include/constants.F'
  double precision :: d(0:max_dim)
  integer,intent(inout) :: nd
  integer, intent(in):: c
@@ -492,7 +492,7 @@ double precision function int_gaus_pol(alpha,n)
 double precision :: alpha
 integer :: n
 double precision :: dble_fact
-include 'constants.F'
+include 'include/constants.F'
 
 !if(iand(n,1).eq.1)then
 !  int_gaus_pol= 0.d0
@@ -521,7 +521,7 @@ double precision function V_r(n,alpha)
 implicit none
 double precision ::  alpha, fact
 integer :: n
-include 'constants.F'
+include 'include/constants.F'
 if(iand(n,1).eq.1)then
  V_r = 0.5d0 * fact(ishft(n,-1)) / (alpha ** (ishft(n,-1) + 1))
 else
@@ -549,7 +549,7 @@ double precision function V_theta(n,m)
 !!     integral on "theta" with boundaries ( 0 ; pi) of [ cos(theta) **n  sin(theta) **m ]
 integer :: n,m,i
 double precision ::  Wallis, prod
-include 'constants.F'
+include 'include/constants.F'
   V_theta = 0.d0
   prod = 1.d0
   do i = 0,ishft(n,-1)-1
@@ -565,7 +565,7 @@ double precision function Wallis(n)
 implicit none
 double precision :: fact
 integer :: n,p
-include 'constants.F'
+include 'include/constants.F'
 if(iand(n,1).eq.0)then
   Wallis = fact(ishft(n,-1))
   Wallis = pi * fact(n) / (dble(ibset(0_8,n)) * (Wallis+Wallis)*Wallis) 

src/Integrals_Monoelec/pot_ao_ints.irp.f

@@ -20,6 +20,51 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`davidson_diag_hjj_mrcc <https://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L51>`_
+  Davidson diagonalization with specific diagonal elements of the H matrix
+  .br
+  H_jj : specific diagonal H matrix elements to diagonalize de Davidson
+  .br
+  dets_in : bitmasks corresponding to determinants
+  .br
+  u_in : guess coefficients on the various states. Overwritten
+  on exit
+  .br
+  dim_in : leftmost dimension of u_in
+  .br
+  sze : Number of determinants
+  .br
+  N_st : Number of eigenstates
+  .br
+  iunit : Unit for the I/O
+  .br
+  Initial guess vectors are not necessarily orthonormal
+
+`davidson_diag_mrcc <https://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L1>`_
+  Davidson diagonalization.
+  .br
+  dets_in : bitmasks corresponding to determinants
+  .br
+  u_in : guess coefficients on the various states. Overwritten
+  on exit
+  .br
+  dim_in : leftmost dimension of u_in
+  .br
+  sze : Number of determinants
+  .br
+  N_st : Number of eigenstates
+  .br
+  iunit : Unit number for the I/O
+  .br
+  Initial guess vectors are not necessarily orthonormal
+
+`h_u_0_mrcc <https://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L355>`_
+  Computes v_0 = H|u_0>
+  .br
+  n : number of determinants
+  .br
+  H_jj : array of <j|H|j>
+
 `mrcc <https://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L1>`_
   Undocumented
 

src/MRCC/README.rst

@@ -1,5 +1,5 @@
 .PHONY: default silent
-
+export
 ifneq ($(IN_MAKE),1) 
 
 default:

src/Makefile.common

@@ -2,7 +2,7 @@ OPENMP  =1
 PROFILE =0
 DEBUG  = 0
 
-IRPF90_FLAGS+= --align=32
+IRPF90_FLAGS+= --align=32 
 FC     = ifort -g 
 #FC     = cache_compile.py ifort -g    # Accelerates compilation
 FCFLAGS= 
@@ -13,6 +13,7 @@ FCFLAGS+= -ip
 FCFLAGS+= -opt-prefetch
 FCFLAGS+= -ftz
 MKL=-mkl=parallel 
+NINJA=ninja
 
 ifeq ($(PROFILE),1)
 FC    += -p -g

src/Makefile.config.example

@@ -1,6 +1,7 @@
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
-SRC=perturbation_template.f
+SRC=
+#SRC=perturbation_template.f
 OBJ=
 
 include $(QPACKAGE_ROOT)/src/Makefile.common

src/Perturbation/Makefile

@@ -59,19 +59,25 @@ default: False
 type: integer
 doc: Nb of points of the QMC grid 
 interface: input
-default: 100
+default: 1000
 
 [pseudo_grid_rmax]
 type: double precision
 doc: R_maxof the QMC grid 
 interface: input
-default: 4.0
+default: 10.0
 
-[pseudo_grid]
+[ao_pseudo_grid]
 type: double precision
 doc: QMC grid 
 interface: output
-size: (pseudo.pseudo_grid_size,ao_basis.ao_num,-pseudo.pseudo_lmax:pseudo.pseudo_lmax,0:pseudo.pseudo_lmax,nuclei.nucl_num)
+size: (ao_basis.ao_num,-pseudo.pseudo_lmax:pseudo.pseudo_lmax,0:pseudo.pseudo_lmax,nuclei.nucl_num,pseudo.pseudo_grid_size)
+
+[mo_pseudo_grid]
+type: double precision
+doc: QMC grid 
+interface: output
+size: (ao_basis.ao_num,-pseudo.pseudo_lmax:pseudo.pseudo_lmax,0:pseudo.pseudo_lmax,nuclei.nucl_num,pseudo.pseudo_grid_size)
 
 [pseudo_matrix]
 type: double precision