Merge pull request #141 from issp-center-dev/flag_parameters

skip parameters in dcore_pre

src/dcore/dcore_bse.py

@@ -27,7 +27,7 @@
 
 from dcore._dispatcher import HDFArchive, dyson
 from dcore.dmft_core import DMFTCoreSolver
-from dcore.program_options import create_parser, parse_parameters, delete_parameters, print_parameters
+from dcore.program_options import create_parser, parse_parameters, print_parameters, delete_parameters
 from dcore.tools import *
 from dcore import impurity_solvers
 from .sumkdft_workers.launcher import run_sumkdft
@@ -42,13 +42,10 @@ def to_str(x):
     return x
 
 
-def compare_str_list(list1, list2):
-    if len(list1) != len(list2):
-        return False
+def _compare_str_list(list1, list2):
+    assert len(list1) == len(list2), f"len({list1}) != len({list2})"
     for x, y in zip(list1, list2):
-        if to_str(x) != to_str(y):
-            return False
-    return True
+        assert to_str(x) == to_str(y), f"{to_str(x)} != {to_str(y)}"
 
 
 def calc_g2_in_impurity_model(solver_name, solver_params, mpirun_command, basis_rot, Umat, gf_struct, beta, n_iw,
@@ -279,7 +276,7 @@ def __init__(self, h5_file, bse_info, n_corr_shells, n_flavors, use_spin_orbit,
         assert n_block == len(spin_names)
 
         # NOTE: change the order of spins in HDF5 to meet SumkDFTChi
-        self.block2 = IndexPair2(list(range(n_corr_shells)), sorted(spin_names), only_diagonal1=only_diagonal)
+        self.block2 = IndexPair2(list(range(n_corr_shells)), spin_names, only_diagonal1=only_diagonal)
         self.inner2 = IndexPair(list(range(n_inner)), convert_to_int=True)
         print(" block2 namelist =", self.block2.namelist)
         print(" inner2 namelist =", self.inner2.namelist)
@@ -289,8 +286,8 @@ def __init__(self, h5_file, bse_info, n_corr_shells, n_flavors, use_spin_orbit,
         self.h5bse = h5BSE(h5_file, bse_grp)
         if bse_info == 'check':
             # check equivalence of info
-            #assert compare_str_list(h5bse.get(key=('block_name',)), self.block2.namelist)
-            #assert compare_str_list(h5bse.get(key=('inner_name',)), self.inner2.namelist)
+            _compare_str_list(self.h5bse.get(key=('block_name',)), self.block2.namelist)
+            _compare_str_list(self.h5bse.get(key=('inner_name',)), self.inner2.namelist)
             assert self.h5bse.get(key=('beta',)) == beta
         elif bse_info == 'save':
             # save info
@@ -342,7 +339,7 @@ def save_xloc(self, xloc_ijkl, icrsh):
         self._save_common(xloc_ijkl, icrsh, 'X_loc')
 
     def save_chiloc(self, chiloc_ijkl, icrsh):
-        self._save_common(chiloc_ijkl, icrsh, 'chi_loc')
+        self._save_common(chiloc_ijkl, icrsh, 'chi_loc_in')
 
     def save_gamma0(self, u_mat, icrsh):
 
@@ -411,7 +408,7 @@ def _calc_bse_x0q(self):
         Calc X_0(q)
         """
         print("\n--- dcore_bse - X_0(q)")
-        if self._params['bse']['skip_X0q_if_exists'] and os.path.exists(self._params['bse']['h5_output_file']):
+        if self._params['bse']['skip_X0q']:
             print(" skip")
             return
 
@@ -457,10 +454,16 @@ def calc_num_flavors(_ish):
         # init for saving data into HDF5
         #
         print("\n--- dcore_bse - invoking h5BSE...")
+
+        if os.path.isfile(self._params['bse']['h5_output_file']):
+            bse_info = 'check'
+        else:
+            bse_info = 'save'
+
         bse = SaveBSE(
             n_corr_shells=self._n_corr_shells,
             h5_file=os.path.abspath(self._params['bse']['h5_output_file']),
-            bse_info='check',
+            bse_info=bse_info,
             nonlocal_order_parameter=False,
             use_spin_orbit=self._use_spin_orbit,
             beta=self._beta,
@@ -627,28 +630,29 @@ def dcore_bse(filename, np=1):
     #
     # Construct a parser with default values
     #
-    pars = create_parser(['model', 'system', 'impurity_solver', 'mpi', 'bse'])
-
+    pars = create_parser(["model", "system", "impurity_solver", "mpi", "bse"])
     #
     # Parse keywords and store
     #
     pars.read(filename)
-    p = pars.as_dict()
-    parse_parameters(p)
-    seedname = p["model"]["seedname"]
-    p["mpi"]["num_processes"] = np
+    params = pars.as_dict()
+    parse_parameters(params)
+
+    params["mpi"]["num_processes"] = np
 
     # Delete unnecessary parameters
-    delete_parameters(p, block='model', delete=['bvec'])
-    delete_parameters(p, block='system', retain=['beta', 'n_iw', 'mu', 'fix_mu', 'prec_mu', 'with_dc', 'no_tail_fit'])
+    delete_parameters(params, block='model', delete=['interaction', 'density_density', 'kanamori', 'slater_f', 'slater_uj', 'slater_basis', 'interaction_file', 'local_potential_matrix', 'local_potential_factor'])
+    delete_parameters(params, block='model', delete=['bvec'])
+    delete_parameters(params, block='system', retain=['beta', 'n_iw', 'mu', 'fix_mu', 'prec_mu', 'with_dc', 'no_tail_fit'])
 
     # Summary of input parameters
-    print_parameters(p)
+    print_parameters(params)
 
     #
     # Load DMFT data
     #
-    solver = DMFTBSESolver(seedname, p, output_file=seedname + '.out.h5')
+    seedname = params["model"]["seedname"]
+    solver = DMFTBSESolver(seedname, params, output_file=seedname + '.out.h5')
     if solver.iteration_number == 0:
         raise RuntimeError("Number of iterations is zero!")
     print("Number of iterations :", solver.iteration_number)

src/dcore/dcore_post.py

@@ -477,7 +477,7 @@ def dcore_post(filename, np=1, prefix=None):
     #
     # Delete unnecessary parameters
     #
-    delete_parameters(p, block='model', delete=['interaction', 'density_density', 'kanamori', 'slater_f', 'slater_uj', 'slater_basis', 'local_potential_matrix', 'local_potential_factor'])
+    delete_parameters(p, block='model', delete=['interaction', 'density_density', 'kanamori', 'slater_f', 'slater_uj', 'slater_basis', 'interaction_file', 'local_potential_matrix', 'local_potential_factor'])
 
     # Summary of input parameters
     print_parameters(p)

src/dcore/dcore_pre.py

@@ -44,7 +44,12 @@ def __generate_local_potential(p):
     spin_orbit = p["model"]["spin_orbit"]
 
     # read parameters from DFT data
-    skc = SumkDFTCompat(p["model"]["seedname"] + '.h5')
+    try:
+        skc = SumkDFTCompat(p["model"]["seedname"] + '.h5')
+    except RuntimeError as e:
+        print(f"\nERROR: {e}", file=sys.stderr)
+        print("Generate lattice model by running dcore_pre with skip_lattice=False (default) before generating local potential.", file=sys.stderr)
+        sys.exit(1)
 
     assert skc.n_inequiv_shells == n_inequiv_shells
 
@@ -122,7 +127,7 @@ def dcore_pre(input_filenames):
     #
     # Construct a parser with default values
     #
-    pars = create_parser(['model'])
+    pars = create_parser(['model', 'pre'])
     #
     # Parse keywords and store
     #
@@ -140,44 +145,73 @@ def dcore_pre(input_filenames):
     #
     print_parameters(p)
 
+    print("\n@@@@@@@@@@@@@@@@@@@  Generate Model-HDF5 File  @@@@@@@@@@@@@@@@@@@@")
     #
     # remove HDF5 file if exists
     #
     h5_file = p['model']['seedname'] + '.h5'
-    if p['model']['lattice'] != 'external':
-        if os.path.exists(h5_file):
-            print("\nRemoving the existing model HDF5 file...")
+    if os.path.exists(h5_file):
+        print(f"\nFile '{h5_file}' found")
+        if p['pre']['overwrite']:
+            print("  --> overwritten (overwrite=True)")
+        else:
+            print("  --> replaced (overwrite=False)")
             os.remove(h5_file)
+    else:
+        print(f"\nFile '{h5_file}' is created")
+
 
     #
     # Lattice information
     #   -> create h5_file/dft_input
     #
-    print("\n@@@@@@@@@@@@@@@@@@@  Generate Model-HDF5 File  @@@@@@@@@@@@@@@@@@@@\n")
-    lattice_model = create_lattice_model(p)
-    lattice_model.generate_model_file()
+    print("\nGenerating lattice model including H(k)")
+    print(f"  in {h5_file}/dft_input")
+    if p['pre']['skip_lattice']:
+        print("skip")
+    else:
+        lattice_model = create_lattice_model(p)
+        lattice_model.generate_model_file()
 
     #
     # Interaction
     #   -> create h5_file/DCore/umat
     #
     print("\nGenerating U-matrix")
-    generate_umat(p)
+    print(f"  in {h5_file}/DCore/Umat")
+    if p['pre']['skip_umat']:
+        print("skip")
+    else:
+        generate_umat(p)
 
     #
     # Local potential
     #   -> create h5_file/DCore/local_potential
     #
     print("\nGenerating local potential")
-    __generate_local_potential(p)
+    print(f"  in {h5_file}/DCore/LocalPotential")
+    if p['pre']['skip_local_potential']:
+        print("skip")
+    else:
+        __generate_local_potential(p)
 
     #
     # Check HDF5 file
     #
     print('')
     print('@@@@@@@@@@@@@@@@@@@ Check Model-HDF5 file @@@@@@@@@@@@@@@@@@@@')
-    __check_if_Hk_is_hermite(h5_file)
-    print_local_fields(h5_file)
+
+    print("\nChecking H(k)")
+    if p['pre']['skip_lattice']:
+        print("skip")
+    else:
+        __check_if_Hk_is_hermite(h5_file)
+
+    print("\nLocal Fields")
+    if p['pre']['skip_lattice']:
+        print("skip")
+    else:
+        print_local_fields(h5_file)
 
     #
     # Finish

src/dcore/program_options.py

@@ -84,6 +84,12 @@ def create_parser(target_sections=None):
     parser.add_option("model", "local_potential_matrix", str, "None", "dict of {ish: 'filename'} to specify local potential matrix of ish-th shell")
     parser.add_option("model", "local_potential_factor", str, "1.0", "Prefactors to the local potential matrix (float or list with len=ncor)")
 
+    # [pre]
+    parser.add_option("pre", "skip_lattice", bool, False, "Skip generation of lattice model including H(k) in dcore_pre. If True, data in seedname.h5/dft_input are kept.")
+    parser.add_option("pre", "skip_umat", bool, False, "Skip generation of U matrix in dcore_pre. If True, data in seedname.h5/DCore/Umat are kept.")
+    parser.add_option("pre", "skip_local_potential", bool, False, "Skip generation of local potential in dcore_pre. If True, data in seedname.h5/DCore/LocalPotential are kept.")
+    parser.add_option("pre", "overwrite", bool, True, "Whether seedname.h5 is overwritten. If False, the existing seedname.h5 is repalced.")
+
     # [system]
     parser.add_option("system", "beta", float, 1.0, "Inverse temperature. This parameter is overwritten, if T is given.")
     parser.add_option("system", "T", float, -1.0, "Temperature. If this parameter is given, beta is overwritten by 1/T.")
@@ -148,9 +154,10 @@ def create_parser(target_sections=None):
     parser.add_option("bse", "num_wb", int, 1, "Number of bosonic frequencies (>0)")
     parser.add_option("bse", "num_wf", int, 10, "Number of fermionic frequencies (>0)")
     parser.add_option("bse", "h5_output_file", str, 'dmft_bse.h5', "Output HDF5 file for bse data")
-    parser.add_option("bse", "skip_X0q_if_exists", bool, False, "Skip X_0(q) calc if file already exists")
+    parser.add_option("bse", "skip_X0q_if_exists", bool, False, "[NOT USED] Skip X_0(q) calc if file already exists", OptionStatus.RETIRED)
+    parser.add_option("bse", "skip_X0q", bool, False, "Skip X_0(q) calc")
     parser.add_option("bse", "skip_Xloc", bool, False, "Skip X_loc calc (for RPA)")
-    parser.add_option("bse", "calc_only_chiloc", bool, False, "Calculate only chi_loc but no X_loc (for SCL, rRPA).")
+    parser.add_option("bse", "calc_only_chiloc", bool, False, "Calculate only chi_loc but no X_loc (for SCL, rRPA). Do not activate skip_Xloc when using this option.")
     parser.add_option("bse", "use_temp_file", bool, False, "Whether or not temporary file is used in computing X0_q. This option will reduce the memory footprints.")
     parser.add_option("bse", "X0q_qpoints_saved", str, 'quadrant', "Specifies for which q points X0q are saved in a HDF file. quadrant or path to a q_path.dat file.")
 

src/dcore/sumkdft_compat.py

@@ -29,7 +29,7 @@ def read_dft_input_data(file, subgrp, things_to_read):
     values = {}
     with HDFArchive(file, 'r') as ar:
         if not subgrp in ar:
-            raise RuntimeError("subrp " + subgrp + "does not exist in " + file + "!")
+            raise RuntimeError("subgrp " + subgrp + " does not exist in " + file + "!")
         # first read the necessary things:
         for it in things_to_read:
             values[it] = ar[subgrp][it]