issue1475: a small bug of iterdict (generator/lib/cp2k.py) (#1476)

1. The flag in iterdict (generator/lib/cp2k.py) now contains the parent
section name, and fix the problem that the content of multiple sections
with the same name will only be inserted into the first section.
2. Add indent for sections.

now the input generate by make_cp2k_input is look like this:
```
&GLOBAL                                                                                                                                                                                                                  
  PROJECT DPGEN                                                                                                                                                                                                          
  PREFERRED_DIAG_LIBRARY SCALAPACK                                                                                                                                                                                       
&END GLOBAL                                                                                                                                                                                                              
&FORCE_EVAL
  METHOD QS
  STRESS_TENSOR ANALYTICAL
  &DFT #FORCE_EVAL
    BASIS_SET_FILE_NAME EMSL_BASIS_SETS
    POTENTIAL_FILE_NAME POTENTIAL
    CHARGE 0
    UKS TRUE
    &MGRID #DFT #FORCE_EVAL
      CUTOFF 800
      REL_CUTOFF 55
      NGRIDS 4
    &END MGRID #DFT #FORCE_EVAL
    &QS #DFT #FORCE_EVAL
      EPS_DEFAULT 1.0E-12
      METHOD GAPW
    &END QS #DFT #FORCE_EVAL
    &SCF #DFT #FORCE_EVAL
      SCF_GUESS ATOMIC
      EPS_SCF 1.0E-6
      MAX_SCF 50
      &MIXING #SCF #DFT #FORCE_EVAL
        METHOD BROYDEN_MIXING
      &END MIXING #SCF #DFT #FORCE_EVAL
      &PRINT #SCF #DFT #FORCE_EVAL
        &RESTART OFF
        &END RESTART #PRINT #SCF #DFT #FORCE_EVAL
      &END PRINT #SCF #DFT #FORCE_EVAL
      ADD_MOS -1 -1
    &END SCF #DFT #FORCE_EVAL
    &XC #DFT #FORCE_EVAL
      &XC_FUNCTIONAL B3LYP
      &END XC_FUNCTIONAL #XC #DFT #FORCE_EVAL
      &HF #XC #DFT #FORCE_EVAL
        &MEMORY #HF #XC #DFT #FORCE_EVAL
          MAX_MEMORY 2000
        &END MEMORY #HF #XC #DFT #FORCE_EVAL
      &END HF #XC #DFT #FORCE_EVAL
    &END XC #DFT #FORCE_EVAL
    &POISSON #DFT #FORCE_EVAL
      PERIODIC NONE
      POISSON_SOLVER MULTIPOLE
    &END POISSON #DFT #FORCE_EVAL
    RELAX_MULTIPLICITY 0.00001
  &END DFT #FORCE_EVAL
  &SUBSYS #FORCE_EVAL
    &CELL #SUBSYS #FORCE_EVAL
      A 14.39252  0.       0.
      B  0.       20.281213  0.
      C  0.        0.       15.801355
      PERIODIC NONE
    &END CELL #SUBSYS #FORCE_EVAL
    &COORD #SUBSYS #FORCE_EVAL
      @include coord.xyz
    &END COORD #SUBSYS #FORCE_EVAL
    &KIND Cl
      BASIS_SET 6-311G**
      POTENTIAL ALL
    &END KIND #SUBSYS #FORCE_EVAL
    &KIND H
      BASIS_SET 6-311G**
      POTENTIAL ALL
    &END KIND #SUBSYS #FORCE_EVAL
    &KIND C
      BASIS_SET 6-311G**
      POTENTIAL ALL
    &END KIND #SUBSYS #FORCE_EVAL
  &END SUBSYS #FORCE_EVAL
  &PRINT #FORCE_EVAL
    &FORCES ON
    &END FORCES #PRINT #FORCE_EVAL
    &STRESS_TENSOR ON
    &END STRESS_TENSOR #PRINT #FORCE_EVAL
  &END PRINT #FORCE_EVAL
&END FORCE_EVAL
```

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: yohsama

dpgen/generator/lib/cp2k.py

@@ -48,13 +48,15 @@ def update_dict(old_d, update_d):
             old_d[k] = update_d[k]
 
 
-def iterdict(d, out_list, flag=None):
-    """:doc: a recursive expansion of dictionary into cp2k input
+def iterdict(d, out_list, flag=None, indent=0):
+    """
+    :doc: a recursive expansion of dictionary into cp2k input
     :k: current key
     :v: current value
     :d: current dictionary under expansion
     :flag: used to record dictionary state. if flag is None,
     it means we are in top level dict. flag is a string.
+    :indent: intent for current section.
     """
     for k, v in d.items():
         k = str(k)  # cast key into string
@@ -64,16 +66,17 @@ def iterdict(d, out_list, flag=None):
             if flag is None:
                 out_list.append("&" + k)
                 out_list.append("&END " + k)
-                iterdict(v, out_list, k)
+                iterdict(v, out_list, k, indent + 2)
             # flag is not None, now it has name of section
             else:
-                index = out_list.index("&END " + flag)
-                out_list.insert(index, "&" + k)
-                out_list.insert(index + 1, "&END " + k)
-                iterdict(v, out_list, k)
+                index = out_list.index(" " * (indent - 2) + "&END " + flag)
+                out_list.insert(index, " " * indent + "&" + k + " #" + flag)
+                out_list.insert(index + 1, " " * indent + "&END " + k + " #" + flag)
+                # the flag now contains its parent section name, separed by "#".
+                iterdict(v, out_list, k + " #" + flag, indent + 2)
         elif isinstance(v, list):
             #            print("we have encountered the repeat section!")
-            index = out_list.index("&" + flag)
+            index = out_list.index(" " * (indent - 2) + "&" + flag)
             # delete the current constructed repeat section
             del out_list[index : index + 2]
             # do a loop over key and corresponding list
@@ -83,14 +86,22 @@ def iterdict(d, out_list, flag=None):
                 k_tmp_list.append(str(k_tmp))
                 v_list_tmp_list.append(v_tmp)
             for repeat_keyword in zip(*v_list_tmp_list):
-                out_list.insert(index, "&" + flag)
-                out_list.insert(index + 1, "&END " + flag)
+                out_list.insert(index, " " * (indent - 2) + "&" + flag)
+                out_list.insert(index + 1, " " * (indent - 2) + "&END " + flag)
                 for idx, k_tmp in enumerate(k_tmp_list):
                     if k_tmp == "_":
-                        out_list[index] = "&" + flag + " " + repeat_keyword[idx]
+                        out_list[index] = (
+                            " " * (indent - 2)
+                            + "&"
+                            + flag.split(" #")[0]
+                            + " "
+                            + repeat_keyword[idx]
+                        )
                     else:
-                        out_list.insert(index + 1, k_tmp + " " + repeat_keyword[idx])
-
+                        out_list.insert(
+                            index + 1,
+                            " " * (indent) + k_tmp + " " + repeat_keyword[idx],
+                        )
             break
 
         else:
@@ -100,12 +111,14 @@ def iterdict(d, out_list, flag=None):
                 print(k, ":", v)
             else:
                 if k == "_":
-                    index = out_list.index("&" + flag)
-                    out_list[index] = "&" + flag + " " + v
+                    index = out_list.index(" " * (indent - 2) + "&" + flag)
+                    out_list[index] = (
+                        " " * (indent - 2) + "&" + flag.split(" #")[0] + " " + v
+                    )
 
                 else:
-                    index = out_list.index("&END " + flag)
-                    out_list.insert(index, k + " " + v)
+                    index = out_list.index(" " * (indent - 2) + "&END " + flag)
+                    out_list.insert(index, " " * indent + k + " " + v)
 
 
 def make_cp2k_input(sys_data, fp_params):

tests/generator/cp2k_test_ref.inp

@@ -1,60 +1,60 @@
 &GLOBAL
-PROJECT DPGEN
+  PROJECT DPGEN
 &END GLOBAL
 &FORCE_EVAL
-METHOD QS
-STRESS_TENSOR ANALYTICAL
-&DFT
-BASIS_SET_FILE_NAME ./cp2k_basis_pp_file/BASIS_MOLOPT
-POTENTIAL_FILE_NAME ./cp2k_basis_pp_file/GTH_POTENTIALS
-CHARGE 0
-UKS F
-MULTIPLICITY 1
-&MGRID
-CUTOFF 400
-REL_CUTOFF 50
-NGRIDS 4
-&END MGRID
-&QS
-EPS_DEFAULT 1.0E-12
-&END QS
-&SCF
-SCF_GUESS ATOMIC
-EPS_SCF 1.0E-6
-MAX_SCF 50
-&OT
-MINIMIZER DIIS
-PRECONDITIONER FULL_SINGLE_INVERSE
-&END OT
-&END SCF
-&XC
-&XC_FUNCTIONAL PBE
-&END XC_FUNCTIONAL
-&END XC
-&END DFT
-&SUBSYS
-&CELL
-&END CELL
-&COORD
-@include coord.xyz
-&END COORD
-&KIND H
-BASIS_SET DZVP-MOLOPT-GTH
-POTENTIAL GTH-PBE-q1
-&END KIND
-&KIND C
-BASIS_SET DZVP-MOLOPT-GTH
-POTENTIAL GTH-PBE-q4
-&END KIND
-&KIND N
-BASIS_SET DZVP-MOLOPT-GTH
-POTENTIAL GTH-PBE-q5
-&END KIND
-&END SUBSYS
-&PRINT
-&FORCES ON
-&END FORCES
-&STRESS_TENSOR ON
-&END STRESS_TENSOR
-&END PRINT
-&END FORCE_EVAL
+  METHOD QS
+  STRESS_TENSOR ANALYTICAL
+  &DFT #FORCE_EVAL
+    BASIS_SET_FILE_NAME ./cp2k_basis_pp_file/BASIS_MOLOPT
+    POTENTIAL_FILE_NAME ./cp2k_basis_pp_file/GTH_POTENTIALS
+    CHARGE 0
+    UKS F
+    MULTIPLICITY 1
+    &MGRID #DFT #FORCE_EVAL
+      CUTOFF 400
+      REL_CUTOFF 50
+      NGRIDS 4
+    &END MGRID #DFT #FORCE_EVAL
+    &QS #DFT #FORCE_EVAL
+      EPS_DEFAULT 1.0E-12
+    &END QS #DFT #FORCE_EVAL
+    &SCF #DFT #FORCE_EVAL
+      SCF_GUESS ATOMIC
+      EPS_SCF 1.0E-6
+      MAX_SCF 50
+      &OT #SCF #DFT #FORCE_EVAL
+        MINIMIZER DIIS
+        PRECONDITIONER FULL_SINGLE_INVERSE
+      &END OT #SCF #DFT #FORCE_EVAL
+    &END SCF #DFT #FORCE_EVAL
+    &XC #DFT #FORCE_EVAL
+      &XC_FUNCTIONAL PBE
+      &END XC_FUNCTIONAL #XC #DFT #FORCE_EVAL
+    &END XC #DFT #FORCE_EVAL
+  &END DFT #FORCE_EVAL
+  &SUBSYS #FORCE_EVAL
+    &CELL #SUBSYS #FORCE_EVAL
+    &END CELL #SUBSYS #FORCE_EVAL
+    &COORD #SUBSYS #FORCE_EVAL
+      @include coord.xyz
+    &END COORD #SUBSYS #FORCE_EVAL
+    &KIND H
+      BASIS_SET DZVP-MOLOPT-GTH
+      POTENTIAL GTH-PBE-q1
+    &END KIND #SUBSYS #FORCE_EVAL
+    &KIND C
+      BASIS_SET DZVP-MOLOPT-GTH
+      POTENTIAL GTH-PBE-q4
+    &END KIND #SUBSYS #FORCE_EVAL
+    &KIND N
+      BASIS_SET DZVP-MOLOPT-GTH
+      POTENTIAL GTH-PBE-q5
+    &END KIND #SUBSYS #FORCE_EVAL
+  &END SUBSYS #FORCE_EVAL
+  &PRINT #FORCE_EVAL
+    &FORCES ON
+    &END FORCES #PRINT #FORCE_EVAL
+    &STRESS_TENSOR ON
+    &END STRESS_TENSOR #PRINT #FORCE_EVAL
+  &END PRINT #FORCE_EVAL
+&END FORCE_EVAL