Merge pull request #38 from scemama/master

Good

data/list_element.txt

@@ -0,0 +1,118 @@
+1    H    Hydrogen
+2    He   Helium
+3    Li   Lithium
+4    Be   Beryllium
+5    B    Boron
+6    C    Carbon
+7    N    Nitrogen
+8    O    Oxygen
+9    F    Fluorine
+10   Ne   Neon
+11   Na   Sodium
+12   Mg   Magnesium
+13   Al   Aluminum
+14   Si   Silicon
+15   P    Phosphorus
+16   S    Sulfur
+17   Cl   Chlorine
+18   Ar   Argon
+19   K    Potassium
+20   Ca   Calcium
+21   Sc   Scandium
+22   Ti   Titanium
+23   V    Vanadium
+24   Cr   Chromium
+25   Mn   Manganese
+26   Fe   Iron
+27   Co   Cobalt
+28   Ni   Nickel
+29   Cu   Copper
+30   Zn   Zinc
+31   Ga   Gallium
+32   Ge   Germanium
+33   As   Arsenic
+34   Se   Selenium
+35   Br   Bromine
+36   Kr   Krypton
+37   Rb   Rubidium
+38   Sr   Strontium
+39   Y    Yttrium
+40   Zr   Zirconium
+41   Nb   Niobium
+42   Mo   Molybdenum
+43   Tc   Technetium
+44   Ru   Ruthenium
+45   Rh   Rhodium
+46   Pd   Palladium
+47   Ag   Silver
+48   Cd   Cadmium
+49   In   Indium
+50   Sn   Tin
+51   Sb   Antimony
+52   Te   Tellurium
+53   I    Iodine
+54   Xe   Xenon
+55   Cs   Cesium
+56   Ba   Barium
+57   La   Lanthanum
+58   Ce   Cerium
+59   Pr   Praseodymium
+60   Nd   Neodymium
+61   Pm   Promethium
+62   Sm   Samarium
+63   Eu   Europium
+64   Gd   Gadolinium
+65   Tb   Terbium
+66   Dy   Dysprosium
+67   Ho   Holmium
+68   Er   Erbium
+69   Tm   Thulium
+70   Yb   Ytterbium
+71   Lu   Lutetium
+72   Hf   Hafnium
+73   Ta   Tantalum
+74   W    Tungsten
+75   Re   Rhenium
+76   Os   Osmium
+77   Ir   Iridium
+78   Pt   Platinum
+79   Au   Gold
+80   Hg   Mercury
+81   Tl   Thallium
+82   Pb   Lead
+83   Bi   Bismuth
+84   Po   Polonium
+85   At   Astatine
+86   Rn   Radon
+87   Fr   Francium
+88   Ra   Radium
+89   Ac   Actinium
+90   Th   Thorium
+91   Pa   Protactinium
+92   U    Uranium
+93   Np   Neptunium
+94   Pu   Plutonium
+95   Am   Americium
+96   Cm   Curium
+97   Bk   Berkelium
+98   Cf   Californium
+99   Es   Einsteinium
+100  Fm   Fermium
+101  Md   Mendelevium
+102  No   Nobelium
+103  Lr   Lawrencium
+104  Rf   Rutherfordium
+105  Db   Dubnium
+106  Sg   Seaborgium
+107  Bh   Bohrium
+108  Hs   Hassium
+109  Mt   Meitnerium
+110  Ds   Darmstadtium
+111  Rg   Roentgenium
+112  Cn   Copernicium
+113  Uut  Ununtrium
+114  Fl   Flerovium
+115  Uup  Ununpentium
+116  Lv   Livermorium
+117  Uus  Ununseptium
+118  Uuo  Ununoctium

ocaml/Input_determinants_by_hand.ml

@@ -11,7 +11,8 @@ module Determinants_by_hand : sig
       psi_coef               : Det_coef.t array;
       psi_det                : Determinant.t array;
     } with sexp
-  val read  : unit -> t option
+  val read  : unit -> t
+  val read_maybe  : unit -> t option
   val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
@@ -210,13 +211,6 @@ end = struct
 
   let read () =
     if (Ezfio.has_mo_basis_mo_tot_num ()) then
-      let n_det = 
-         read_n_det ()
-      in
-      if ( (Det_number.to_int n_det) > n_det_read_max ) then
-        None
-      else
-        Some
         { n_int                  = read_n_int ()                ;
           bit_kind               = read_bit_kind ()             ;
           n_det                  = read_n_det ()                ;
@@ -224,6 +218,17 @@ end = struct
           psi_coef               = read_psi_coef ()             ;
           psi_det                = read_psi_det ()              ;
         }
+    else
+      failwith "No molecular orbitals, so no determinants"
+  ;;
+
+  let read_maybe () =
+    let n_det = 
+       read_n_det ()
+    in
+    if ( (Det_number.to_int n_det) < n_det_read_max ) then
+      try Some (read ()) with
+      | Failure _ -> None
     else
       None
   ;;

ocaml/TaskServer.ml

@@ -36,7 +36,7 @@ let bind_socket ~socket_type ~socket ~address =
   | 0 -> failwith @@ Printf.sprintf
         "Unable to bind the %s socket : %s "
         socket_type address
-  | -1 -> ();
+  | -1 -> ()
   | i -> 
       try
         ZMQ.Socket.bind socket address;

ocaml/qp_print_basis.ml

@@ -43,9 +43,7 @@ let psi_det () =
     failwith "Error reading EZFIO file";
   Ezfio.set_file ezfio_filename;
   let psi_det =
-    match Input.Determinants_by_hand.read () with
+    Input.Determinants_by_hand.read () 
-    | Some psi_det -> psi_det
-    | _ -> failwith "Error reading the mo set"
   in
   Input.Determinants_by_hand.to_rst psi_det 
   |> Rst_string.to_string
@@ -56,5 +54,5 @@ let psi_det () =
 let () = 
   basis ();
   mo ();
-  psi_det ();
+  psi_det ()
 

ocaml/test_message.ml

@@ -1,7 +1,7 @@
 open Core.Std
 
 let () =
-  Message.of_string "new_job tcp://127.0.0.1 inproc://ao_ints:12345 ao_integrals"
+  Message.of_string "new_job ao_integrals tcp://127.0.0.1 inproc://ao_ints:12345"
   |> Message.to_string 
   |> print_endline
   ;
@@ -37,7 +37,7 @@ let () =
   ;
 
   try
-    Message.of_string "new_job inproc://ao_ints tcp://127.0.0.1:12345 ao_integrals"
+    Message.of_string "new_job ao_integrals inproc://ao_ints tcp://127.0.0.1:12345"
     |> Message.to_string 
     |> print_endline
     ;

plugins/qmcpack/qp_convert_qmcpack_to_ezfio.py

@@ -9,6 +9,7 @@ print "#QP -> QMCPACK"
 
 from ezfio import ezfio
 
+import os
 import sys
 ezfio_path = sys.argv[1]
 
@@ -17,7 +18,15 @@ ezfio.set_file(ezfio_path)
 do_pseudo = ezfio.get_pseudo_do_pseudo()
 if do_pseudo:
     print "do_pseudo True"
-    print "The charge of nucl will be decreasced for taking into acount the pseudo potentiel"
+    from qp_path import QP_ROOT
+
+    l_ele_path = os.path.join(QP_ROOT,"data","list_element.txt")
+    with open(l_ele_path, "r") as f:
+        data_raw = f.read()
+
+    l_element_raw = data_raw.split("\n")
+    l_element = [element_raw.split() for element_raw in l_element_raw]
+    d_z = dict((abr, z) for (z, abr, ele) in l_element)
 else:
     print "do_pseudo False"
 
@@ -68,7 +77,10 @@ print "nucl_num", len(l_label)
 print "Atomic coord in Bohr"
 
 for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
-    print list_to_string(t)
+    t_1 = d_z[t[0]] if do_pseudo else t[1]
+    
+    t_new = [t[0],t_1,t[2]]
+    print list_to_string(t_new)
 
 #
 # Call externet process to get the sysmetry
@@ -79,7 +91,6 @@ process = subprocess.Popen(
     stdout=subprocess.PIPE)
 out, err = process.communicate()
 
-print len(out.split("\n\n\n"))
 basis_raw, sym_raw, _ , det_raw, _ = out.split("\n\n\n")
 
 #  _                 __        
@@ -310,8 +321,8 @@ if do_pseudo:
             if l_dump:
                 l_str.append(l_dump)
 
-        str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE -1 AND LMAX {2} ARE"
+        str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
-        print str_.format(a, i + 1, int(len(l_str) - 1))
+        print str_.format(a, i + 1, int(d_z[a])-int(l_charge[i]), int(len(l_str) - 1))
 
         for i, l in enumerate(l_str):
             str_ = "FOR L= {0} COEFF N ZETA"
@@ -319,7 +330,8 @@ if do_pseudo:
             for ii, ll in enumerate(l):
                 print " ", ii + 1, ll
 
-    str_ = "THE ECP RUN REMOVES -1 CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
+    str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
+    print str_.format(sum([int(d_z[a])-int(l_charge[i]) for i,a in enumerate(l_label)]))
     print "END_PSEUDO"
 
 #  _         

plugins/qmcpack/save_for_qmcpack.irp.f

@@ -14,6 +14,12 @@ program qmcpack
     enddo
   enddo
   call ezfio_set_ao_basis_ao_coef(ao_coef)
+  do j=1,mo_tot_num
+    do i=1,ao_num
+      mo_coef(i,j) *= 1.d0/ao_coef_normalization_factor(i)
+    enddo
+  enddo
+  call save_mos
   call system('rm '//trim(ezfio_filename)//'/mo_basis/ao_md5')
   call system('$QP_ROOT/src/qmcpack/qp_convert_qmcpack_to_ezfio.py '//trim(ezfio_filename))
 

scripts/ezfio_interface/qp_edit_template

@@ -75,7 +75,7 @@ let get s =
          | Ao_basis ->
            f Ao_basis.(read, to_rst)
          | Determinants_by_hand ->
-           f Determinants_by_hand.(read, to_rst)
+           f Determinants_by_hand.(read_maybe, to_rst)
 {section_to_rst}
       end
     with

src/AO_Basis/aos.irp.f

@@ -52,9 +52,6 @@ END_PROVIDER
      enddo
     enddo
     ao_coef_normalization_factor(i) = 1.d0/sqrt(norm)
-    do j=1,ao_prim_num(i)
-      ao_coef_normalized(i,j) = ao_coef_normalized(i,j) * ao_coef_normalization_factor(i)
-    enddo
   enddo
 
 END_PROVIDER