Merge pull request #3 from kousuke-nakano/devel

Initial public release of turbogenius

.github/CODEOWNERS

@@ -0,0 +1,4 @@
+# These owners are the default owners for everything in
+# the repo. Unless a later match takes precedence,
+* @kousuke-nakano
+

README.md

@@ -107,25 +107,16 @@ and type `make html`. The document is generated in `docs/_build/html`.
 `index.html` is the main page.
 
 # Reference
-K. Nakano et. al in prepareation (2022).
+K. Nakano et. al in prepareation (2023).
 
 # How to contribute
 
-Work on the development or on a new branch
+Please do not directly push your changes to `main` and `devel` branch.
+Please create a pull request on GitHub from your forked repository or a new branch (e.g. `devel-#1`). 
 
-    git merge <new branch> development # if you work on a new branch.
-    git push origin development
-
-Check the next-version version
+# How to check the version info.
 
     # Confirm the version number via `setuptools-scm`
     python -m setuptools_scm
     e.g., 1.1.4.dev28+gceef293.d20221123 -> <next-version> = v1.1.4 or v1.1.4-alpha(for pre-release)
 
-Add and push with the new tag
-
-    # Push with tag
-    git tag <next-version>  # e.g., git tag v1.1.4  # Do not forget "v" before the version number!
-    git push origin development --tags  # or to the new branch
-
-Send a pull request to the main branch on GitHub. 

setup.cfg

@@ -24,22 +24,22 @@ classifiers =
 zip_safe = False
 include_package_data = True
 packages = find:
-python_requires = >="3.7.2"
+python_requires = >=3.7.2
 install_requires =
-    matplotlib  >= "3.1.1"
-    numpy       >= "1.20.1"
-    pandas      >= "1.2.2"
-    ase         >= "3.21.0"
-    trexio      >= "1.2.0"
-    pymatgen    >= "2021.2.16"
-    pytest      >= "5.2.1"
-    gitpython   >= "3.1.27"
-    pydriller   >= "2.1"
-    basis-set-exchange >= "0.9"
-    click       >= "8.1.3"
-    tqdm        >= "4.36.1"
-    setuptools_scm >= "7.0.5"
-    psutil      >= "5.0.0"
+    matplotlib  >= 3.1.1
+    numpy       >= 1.20.1
+    pandas      >= 1.2.2
+    ase         >= 3.21.0
+    trexio      >= 1.2.0
+    pymatgen    >= 2021.2.16
+    pytest      >= 5.2.1
+    gitpython   >= 3.1.27
+    pydriller   >= 2.1
+    basis-set-exchange >= 0.9
+    click       >= 8.1.3
+    tqdm        >= 4.36.1
+    setuptools_scm >= 7.0.5
+    psutil      >= 5.0.0
 
 [options.package_data]
 * = *.txt, *.rst

turbogenius/convertfort10_genius.py

@@ -13,6 +13,7 @@
 # python modules
 import os
 import numpy as np
+from typing import Optional
 
 # Logger
 from logging import getLogger, StreamHandler, Formatter
@@ -77,13 +78,12 @@ def __init__(
             self.convertfort10.comment_out(parameter="ny")
             self.convertfort10.comment_out(parameter="nz")
         else:
-            # +- 7.5 bohr from the edges.
             pos = self.io_fort10.f10structure.positions
-            Lx = np.max(pos[:, 0]) - np.min(pos[:, 0]) + 3.0
-            Ly = np.max(pos[:, 1]) - np.min(pos[:, 1]) + 3.0
-            Lz = np.max(pos[:, 2]) - np.min(pos[:, 2]) + 3.0
+            Lx = np.max(pos[:, 0]) - np.min(pos[:, 0]) + 6.0
+            Ly = np.max(pos[:, 1]) - np.min(pos[:, 1]) + 6.0
+            Lz = np.max(pos[:, 2]) - np.min(pos[:, 2]) + 6.0
             logger.info(
-                "Lbox is set to +- 1.5 bohr from the edges of the molecules."
+                "Lbox is set to +- 3.0 bohr from the edges of the molecules."
             )
             logger.info(f"Lx={Lx}, Ly={Ly}, Lz={Lz}")
             ax = self.grid_size
@@ -150,7 +150,7 @@ def run(self, input_name="convertfort10.input", output_name="out_conv"):
         flags = self.convertfort10.check_results(output_names=[output_name])
         assert all(flags)
 
-    def check_results(self, output_names: list = ["out_conv"]) -> bool:
+    def check_results(self, output_names: Optional[list] = None) -> bool:
         """
         Check the result.
 
@@ -159,6 +159,8 @@ def check_results(self, output_names: list = ["out_conv"]) -> bool:
         Returns:
             bool: True if all the runs were successful, False if an error is detected in the files.
         """
+        if output_names is None:
+            output_names = ["out_conv"]
         return self.convertfort10.check_results(output_names=output_names)
 
 

turbogenius/convertfort10mol_genius.py

@@ -13,6 +13,7 @@
 # python modules
 import os
 import numpy as np
+from typing import Optional
 
 # Logger
 from logging import getLogger, StreamHandler, Formatter
@@ -40,10 +41,10 @@ class Convertfort10mol_genius(GeniusIO):
 
     def __init__(
         self,
-        fort10="fort.10_in",
-        add_random_mo=True,
-        grid_size=0.10,
-        additional_mo=0,
+        fort10: str = "fort.10_in",
+        add_random_mo: bool = True,
+        grid_size: float = 0.10,
+        additional_mo: int = 0,
     ):
 
         self.fort10 = fort10
@@ -178,7 +179,7 @@ def run(
         flags = self.convertfort10mol.check_results(output_names=[output_name])
         assert all(flags)
 
-    def check_results(self, output_names: list = ["out_mol"]) -> bool:
+    def check_results(self, output_names: Optional[list] = None) -> bool:
         """
         Check the result.
 
@@ -187,6 +188,8 @@ def check_results(self, output_names: list = ["out_mol"]) -> bool:
         Return:
             bool: True if all the runs were successful, False if an error is detected in the files.
         """
+        if output_names is None:
+            output_names = ["out_mol"]
         return self.convertfort10mol.check_results(output_names=output_names)
 
 

turbogenius/convertpfaff_genius.py

@@ -10,6 +10,7 @@
 
 # python modules
 import os
+from typing import Optional
 
 # Logger
 from logging import getLogger, StreamHandler, Formatter
@@ -95,7 +96,7 @@ def run(
         flags = self.convertpfaff.check_results(output_names=[output_name])
         assert all(flags)
 
-    def check_results(self, output_names: list = ["out_pfaff"]) -> bool:
+    def check_results(self, output_names: Optional[list] = None) -> bool:
         """
         Check the result.
 
@@ -104,6 +105,8 @@ def check_results(self, output_names: list = ["out_pfaff"]) -> bool:
         Returns:
             bool: True if all the runs were successful, False if an error is detected in the files.
         """
+        if output_names is None:
+            output_names = ["out_pfaff"]
         return self.convertpfaff.check_results(output_names=output_names)
 
 

turbogenius/correlated_sampling_genius.py

@@ -12,6 +12,7 @@
 
 # python modules
 import os
+from typing import Optional
 
 # Logger
 from logging import getLogger, StreamHandler, Formatter
@@ -52,8 +53,10 @@ def __init__(
         num_walkers: int = -1,  # default -1 -> num of MPI process.
         maxtime: int = 172800,
         twist_average: bool = False,
-        kpoints: list = [1, 1, 1, 0, 0, 0],
+        kpoints: Optional[list] = None,
     ):
+        if kpoints is None:
+            kpoints = [1, 1, 1, 0, 0, 0]
 
         self.in_fort10 = in_fort10
         self.corr_fort10 = corr_fort10
@@ -244,8 +247,8 @@ def run(
 
     def check_results(
         self,
-        vmc_output_names: list = ["out_vmc"],
-        readforward_output_names: list = ["out_readforward"],
+        vmc_output_names: Optional[list] = None,
+        readforward_output_names: Optional[list] = None,
     ) -> bool:
         """
         Check the result.
@@ -256,6 +259,10 @@ def check_results(
         Returns:
             bool: True if all the runs were successful, False if an error is detected in the files.
         """
+        if vmc_output_names is None:
+            vmc_output_names = ["out_vmc"]
+        if readforward_output_names is None:
+            readforward_output_names = ["out_readforward"]
         return self.readforward.check_results(
             output_names=readforward_output_names
         ) + self.vmc.check_results(output_names=vmc_output_names)

turbogenius/lrdmc_genius.py

@@ -12,6 +12,7 @@
 
 # python modules
 import os
+from typing import Optional
 
 # Logger
 from logging import getLogger, StreamHandler, Formatter
@@ -34,6 +35,7 @@ class LRDMC_genius(GeniusIO):
          fort10 (str): fort.10 WF file
          lrdmcsteps (int): total number of MCMC steps.
          alat (float): Lattice space (Bohr)
+         time_branching: interval between two branching steps. (a.u.)
          etry (float): Trial Energy (Ha)
          num_walkers (int): The number of walkers, -1 (default) = the number of MPI processes
          maxtime (int): Maxtime (sec.)
@@ -48,14 +50,17 @@ def __init__(
         fort10: str = "fort.10",
         lrdmcsteps: int = 100,
         alat: float = -0.20,
+        time_branching: float = 0.10,
         etry: float = 0.0,
         num_walkers: int = -1,  # default -1 -> num of MPI process.
         maxtime: int = 172800,
         twist_average: bool = False,
-        kpoints: list = [1, 1, 1, 0, 0, 0],
+        kpoints: Optional[list] = None,
         force_calc_flag: bool = False,
-        nonlocalmoves: str = "tmove",  # tmove, dla, dlatm
+        nonlocalmoves: str = "dla",  # tmove, dla, dlatm
     ):
+        if kpoints is None:
+            kpoints = [1, 1, 1, 0, 0, 0]
 
         self.force_calc_flag = force_calc_flag
         self.twist_average = twist_average
@@ -88,7 +93,9 @@ def __init__(
         self.lrdmc.set_parameter(
             parameter="alat", value=alat, namelist="&dmclrdmc"
         )
-
+        self.lrdmc.set_parameter(
+            parameter="tbra", value=time_branching, namelist="&dmclrdmc"
+        )
         typereg, npow = get_nonlocalmoves_setting(nonlocalmoves=nonlocalmoves)
         self.lrdmc.set_parameter(
             parameter="typereg", value=typereg, namelist="&dmclrdmc"
@@ -257,7 +264,7 @@ def store_result(
         bin_block: int = 10,
         warmupblocks: int = 2,
         correcting_factor: int = 2,
-        output_names: list = ["out_fn"],
+        output_names: Optional[list] = None,
         rerun: bool = False,
     ) -> None:
         """
@@ -271,6 +278,8 @@ def store_result(
             output_names (list): a list of output file names
             rerun (bool): if true, compute energy and force again even if there are energy and force files.
         """
+        if output_names is None:
+            output_names = ["out_fn"]
         self.estimated_time_for_1_generation = (
             self.get_estimated_time_for_1_generation(output_names=output_names)
         )
@@ -305,7 +314,7 @@ def compute_energy_and_forces(
         )
 
     def get_estimated_time_for_1_generation(
-        self, output_names: list = ["out_fn"]
+        self, output_names: Optional[list] = None
     ) -> float:
         """
         This procedure stores estimated_time_for_1_generation.
@@ -316,11 +325,13 @@ def get_estimated_time_for_1_generation(
         Return:
             float: estimated_time_for_1_generation.
         """
+        if output_names is None:
+            output_names = ["out_fn"]
         return self.lrdmc.get_estimated_time_for_1_generation(
             output_names=output_names
         )
 
-    def check_results(self, output_names: list = ["out_fn"]) -> bool:
+    def check_results(self, output_names: Optional[list] = None) -> bool:
         """
         Check the result.
 
@@ -329,6 +340,8 @@ def check_results(self, output_names: list = ["out_fn"]) -> bool:
         Return:
             bool: True if all the runs were successful, False if an error is detected in the files.
         """
+        if output_names is None:
+            output_names = ["out_fn"]
         return self.lrdmc.check_results(output_names=output_names)