updated bin

bin/qp_convert_output_to_ezfio

@@ -121,6 +121,7 @@ def write_ezfio(res, filename):
     exponent = []
 
     res.convert_to_cartesian()
+
     # ~#~#~#~#~#~#~ #
     # P a r s i n g #
     # ~#~#~#~#~#~#~ #
@@ -178,6 +179,72 @@ def write_ezfio(res, filename):
 
     print("OK")
 
+    #   _
+    #  |_)  _.  _ o  _
+    #  |_) (_| _> | _>
+    #
+
+    print("Basis\t\t...\t", end=' ')
+    # ~#~#~#~ #
+    # I n i t #
+    # ~#~#~#~ #
+
+    coefficient = []
+    exponent = []
+
+    # ~#~#~#~#~#~#~ #
+    # P a r s i n g #
+    # ~#~#~#~#~#~#~ #
+
+    inucl = {}
+    for i, a in enumerate(res.geometry):
+       inucl[a.coord] = i
+
+    nbasis = 0
+    nucl_index = []
+    curr_center = -1
+    nucl_shell_num = []
+    ang_mom = []
+    nshell = 0
+    nshell_tot = 0
+    shell_index = []
+    shell_prim_num = []
+    for b in res.basis:
+        s = b.sym
+        if str.count(s, "y") + str.count(s, "x") == 0:
+          c = inucl[b.center]
+          nshell += 1
+          nshell_tot += 1
+          if c != curr_center:
+             curr_center = c
+             nucl_shell_num.append(nshell)
+             nshell = 0
+          nbasis += 1
+          nucl_index.append(c+1)
+          coefficient += b.coef[:len(b.prim)]
+          exponent += [p.expo for p in b.prim]
+          ang_mom.append(str.count(s, "z"))
+          shell_prim_num.append(len(b.prim))
+          shell_index += [nshell_tot+1] * len(b.prim)
+
+    # ~#~#~#~#~ #
+    # W r i t e #
+    # ~#~#~#~#~ #
+
+    ezfio.set_basis_basis("Read from ResultsFile")
+    ezfio.set_basis_shell_num(len(ang_mom))
+    ezfio.set_basis_basis_nucleus_index(nucl_index)
+    ezfio.set_basis_prim_num(len(coefficient))
+
+    ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
+    ezfio.set_basis_prim_coef(coefficient)
+    ezfio.set_basis_prim_expo(exponent)
+    ezfio.set_basis_shell_ang_mom(ang_mom)
+    ezfio.set_basis_shell_prim_num(shell_prim_num)
+    ezfio.set_basis_shell_index(shell_index)
+
+    print("OK")
+
     #                _
     # |\/|  _   _   |_)  _.  _ o  _
     # |  | (_) _>   |_) (_| _> | _>
@@ -227,12 +294,17 @@ def write_ezfio(res, filename):
     for i in range(mo_num):
         energies.append(MOs[i].eigenvalue)
 
+    OccNum = []
     if res.occ_num is not None:
-        OccNum = []
         for i in MOindices:
             OccNum.append(res.occ_num[MO_type][i])
+    else:
+        for i in range(res.num_beta):
+            OccNum.append(2.)
+        for i in range(res.num_beta,res.num_alpha):
+            OccNum.append(1.)
 
-        while len(OccNum) < mo_num:
+    while len(OccNum) < mo_num:
             OccNum.append(0.)
 
     MoMatrix = []
@@ -255,8 +327,9 @@ def write_ezfio(res, filename):
     # ~#~#~#~#~ #
 
     ezfio.set_mo_basis_mo_num(mo_num)
-    ezfio.set_mo_basis_mo_occ(OccNum)
     ezfio.set_mo_basis_mo_coef(MoMatrix)
+    ezfio.set_mo_basis_mo_occ(OccNum)
+
     print("OK")
 
 
@@ -317,8 +390,6 @@ def write_ezfio(res, filename):
         n_beta = res.num_beta
         for i in range(nucl_num):
             charge[i] -= nucl_charge_remove[i]
-            n_alpha -= nucl_charge_remove[i]/2
-            n_beta -= nucl_charge_remove[i]/2
         ezfio.set_nuclei_nucl_charge(charge)
         ezfio.set_electrons_elec_alpha_num(n_alpha)
         ezfio.set_electrons_elec_beta_num(n_beta)

bin/qp_export_as_tgz

@@ -99,7 +99,9 @@ function find_libs () {
 }
 
 function find_exec () {
-  find ${QP_ROOT}/$1 -perm /u+x -type f
+  for i in $@ ; do
+     find ${QP_ROOT}/$i -perm /u+x -type f
+  done
 }
 
 
@@ -119,7 +121,7 @@ fi
 echo "Copying binary files"
 #     --------------------
 
-FORTRAN_EXEC=$(find_exec src)
+FORTRAN_EXEC=$(find_exec src/*/)
 if [[ -z $FORTRAN_EXEC ]] ; then
   error 'No Fortran binaries found.'
   exit 1

bin/qp_name

@@ -30,7 +30,7 @@ try:
     from docopt import docopt
     from qp_path import QP_SRC, QP_ROOT
 except ImportError:
-    print("source .quantum_package.rc")
+    print("source quantum_package.rc")
     raise
 
 

bin/qp_plugins

@@ -6,6 +6,7 @@ Usage:
        qp_plugins download <url> [-n <name>]
        qp_plugins install <name>...
        qp_plugins uninstall <name>
+       qp_plugins remove    <name>
        qp_plugins update [-r <repo>]
        qp_plugins create -n <name> [-r <repo>] [<needed_modules>...]
 
@@ -24,6 +25,8 @@ Options:
 
     uninstall                 Uninstall a plugin
 
+    remove                    Uninstall a plugin
+
     update                    Update the repository 
 
     create
@@ -274,7 +277,7 @@ def main(arguments):
             subprocess.check_call(["qp_create_ninja", "update"])
             print("[ OK ]")
 
-    elif arguments["uninstall"]:
+    elif arguments["uninstall"] or arguments["remove"]:
 
         m_instance = ModuleHandler([QP_SRC])
         d_descendant = m_instance.dict_descendant

bin/qp_set_frozen_core

@@ -7,12 +7,13 @@ setting all MOs as Active, except the n/2 first ones which are set as Core.
 If pseudo-potentials are used, all the MOs are set as Active.
 
 Usage:
-      qp_set_frozen_core [-q|--query] [(-l|-s|--large|--small)] EZFIO_DIR
+      qp_set_frozen_core [-q|--query] [(-l|-s|-u|--large|--small|--unset)] EZFIO_DIR
 
 Options:
     -q --query   Prints in the standard output the number of frozen MOs
     -l --large   Use a small core
     -s --small   Use a large core
+    -u --unset   Unset frozen core
 
 
 Default numbers of frozen electrons:
@@ -49,7 +50,7 @@ import os.path
 try:
     import qp_path
 except ImportError:
-    print("source .quantum_package.rc")
+    print("source quantum_package.rc")
     raise
 
 from docopt import docopt
@@ -88,7 +89,9 @@ def main(arguments):
                 elif charge <=  54: n_frozen += 9
                 elif charge <=  86: n_frozen += 18
                 elif charge <= 118: n_frozen += 27
+        elif arguments["--unset"]:
 
+              n_frozen = 0
         else:  # default                                                                      
             for charge in ezfio.nuclei_nucl_charge:
                 if   charge <=   4: pass

bin/qp_set_frozen_large_core

@@ -23,7 +23,7 @@ import os.path
 try:
     import qp_path
 except ImportError:
-    print("source .quantum_package.rc")
+    print("source quantum_package.rc")
     raise
 
 from docopt import docopt