From 9a417bb349f74a6212b6e48401532d8e5cb66d81 Mon Sep 17 00:00:00 2001 From: alongd Date: Sat, 27 Jul 2024 10:28:32 +0000 Subject: [PATCH] deploy: df19d8fb8af1221b3b293c88ea0eb50d0a4663b7 --- _modules/arc/common.html | 3 ++- _modules/arc/level.html | 33 +++++++++++++++++++++++---------- _modules/arc/main.html | 27 +++++++++++++-------------- _modules/arc/utils/scale.html | 14 +++----------- api/level.html | 19 ++++++++++++++++++- genindex.html | 2 ++ objects.inv | Bin 6968 -> 6984 bytes searchindex.js | 2 +- 8 files changed, 62 insertions(+), 38 deletions(-) diff --git a/_modules/arc/common.html b/_modules/arc/common.html index e06566b842..8dacca6822 100644 --- a/_modules/arc/common.html +++ b/_modules/arc/common.html @@ -1867,9 +1867,10 @@

Source code for arc.common

 
     for element, count in element_dict_mol.items():
         if element not in element_dict_xyz or element_dict_xyz[element] != count:
-           return False
+            return False
     return True
+
[docs]def convert_to_hours(time_str:str) -> float: """Convert walltime string in format HH:MM:SS to hours. diff --git a/_modules/arc/level.html b/_modules/arc/level.html index 85d537f0eb..de6292fbce 100644 --- a/_modules/arc/level.html +++ b/_modules/arc/level.html @@ -173,7 +173,6 @@

Source code for arc.level

 
 import arkane.encorr.data as arkane_data
 from arkane.encorr.bac import BAC
-from arkane.encorr.corr import assign_frequency_scale_factor
 from arkane.modelchem import METHODS_THAT_REQUIRE_SOFTWARE, LevelOfTheory, standardize_name
 
 from arc.common import ARC_PATH, get_logger, get_ordered_intersection_of_two_lists, read_yaml_file
@@ -223,7 +222,7 @@ 
Source code for arc.level
                  method_type: Optional[str] = None,
                  software: Optional[str] = None,
                  software_version: Optional[Union[int, float, str]] = None,
-                 compatible_ess: Optional[List[str, ...]] = None,
+                 compatible_ess: Optional[List[str]] = None,
                  solvation_method: Optional[str] = None,
                  solvent: Optional[str] = None,
                  solvation_scheme_level: Optional[Level] = None,
@@ -318,8 +317,6 @@ 
Source code for arc.level
                 for key, arg in self.args.items():
                     if key == 'keyword':
                         str_ += f' {arg}'
-        if self.method_type is not None:
-            str_ += f' ({self.method_type})'
         return str_
 
 
[docs]    def copy(self):
@@ -562,12 +559,7 @@ 
Source code for arc.level
                 var_1 = None
 
             if variant == 'freq':
-                # if not found, the factor is set to exactly 1
-                if assign_frequency_scale_factor(level_of_theory=var_1) != 1:
-                    return var_1
-                if assign_frequency_scale_factor(level_of_theory=var_2) != 1:
-                    return var_2
-                return None
+                return var_2
 
             if variant == 'AEC':
                 try:
@@ -737,6 +729,27 @@ 
Source code for arc.level
             splits = arkane_level.split(f"{key}='")
             level_dict[key] = splits[1].split("'")[0]
     return level_dict

+
+
+
[docs]def assign_frequency_scale_factor(level: Union[str, Level]) -> Optional[int]:
+    """
+    Assign a frequency scaling factor to a level of theory.
+
+    Args:
+        level (Union[str, Level]): The level of theory.
+
+    Returns:
+        Optional[int]: The frequency scaling factor.
+    """
+    freq_scale_factors = read_yaml_file(os.path.join(ARC_PATH, 'data', 'freq_scale_factors.yml'))['freq_scale_factors']
+    if isinstance(level, str):
+        if level in freq_scale_factors:
+            return freq_scale_factors[level]
+        level = Level(repr=level)
+    level_str = str(level)
+    if level_str in freq_scale_factors:
+        return freq_scale_factors[level_str]
+    return None

 

 
            

diff --git a/_modules/arc/main.html b/_modules/arc/main.html
index 294e0a49f6..9ed752ff42 100644
--- a/_modules/arc/main.html
+++ b/_modules/arc/main.html
@@ -182,7 +182,6 @@ 
Source code for arc.main
 from IPython.display import display
 from typing import Dict, List, Optional, Tuple, Union
 
-from arkane.encorr.corr import assign_frequency_scale_factor
 from rmgpy.reaction import Reaction
 from rmgpy.species import Species
 
@@ -201,7 +200,7 @@ 
Source code for arc.main
                         )
 from arc.exceptions import InputError, SettingsError, SpeciesError
 from arc.imports import settings
-from arc.level import Level
+from arc.level import Level, assign_frequency_scale_factor
 from arc.job.factory import _registered_job_adapters
 from arc.job.ssh import SSHClient
 from arc.processor import process_arc_project
@@ -668,7 +667,8 @@ 
Source code for arc.main
                 if not isinstance(self.freq_level, (dict, str)) else self.freq_level
         if self.freq_scale_factor is not None:
             restart_dict['freq_scale_factor'] = self.freq_scale_factor
-        if self.irc_level is not None and str(self.irc_level).split()[0] != default_levels_of_theory['irc']:
+        if self.irc_level is not None and len(self.irc_level.method) \
+                and str(self.irc_level).split()[0] != default_levels_of_theory['irc']:
             restart_dict['irc_level'] = self.irc_level.as_dict() \
                 if not isinstance(self.irc_level, (dict, str)) else self.irc_level
         if self.keep_checks:
@@ -685,7 +685,8 @@ 
Source code for arc.main
         if self.opt_level is not None and str(self.opt_level).split()[0] != default_levels_of_theory['opt']:
             restart_dict['opt_level'] = self.opt_level.as_dict() \
                 if not isinstance(self.opt_level, (dict, str)) else self.opt_level
-        if self.orbitals_level is not None and str(self.orbitals_level).split()[0] != default_levels_of_theory['orbitals']:
+        if self.orbitals_level is not None and len(self.orbitals_level.method) \
+                and str(self.orbitals_level).split()[0] != default_levels_of_theory['orbitals']:
             restart_dict['orbitals_level'] = self.orbitals_level.as_dict() \
                 if not isinstance(self.orbitals_level, (dict, str)) else self.orbitals_level
         if self.output:
@@ -697,10 +698,12 @@ 
Source code for arc.main
             restart_dict['reactions'] = [rxn.as_dict() for rxn in self.reactions]
         if self.running_jobs:
             restart_dict['running_jobs'] = self.running_jobs
-        if self.scan_level is not None and str(self.scan_level).split()[0] != default_levels_of_theory['scan']:
+        if self.scan_level is not None and len(self.scan_level.method) \
+                and str(self.scan_level).split()[0] != default_levels_of_theory['scan']:
             restart_dict['scan_level'] = self.scan_level.as_dict() \
                 if not isinstance(self.scan_level, (dict, str)) else self.scan_level
-        if self.sp_level is not None and str(self.sp_level).split()[0] != default_levels_of_theory['sp']:
+        if self.sp_level is not None and len(self.sp_level.method) \
+                and str(self.sp_level).split()[0] != default_levels_of_theory['sp']:
             restart_dict['sp_level'] = self.sp_level.as_dict() \
                 if not isinstance(self.sp_level, (dict, str)) else self.sp_level
         restart_dict['species'] = [spc.as_dict() for spc in self.species]
@@ -1070,16 +1073,12 @@ 
Source code for arc.main
             freq_level = self.composite_method if self.composite_method is not None \
                 else self.freq_level if self.freq_level is not None else None
             if freq_level is not None:
-                arkane_freq_lot = freq_level.to_arkane_level_of_theory(variant='freq')
-                if arkane_freq_lot is not None:
-                    # Arkane has this harmonic frequencies scaling factor.
-                    self.freq_scale_factor = assign_frequency_scale_factor(level_of_theory=arkane_freq_lot)
-                else:
-                    logger.info(f'Could not determine the harmonic frequencies scaling factor for '
-                                f'{arkane_freq_lot} from Arkane.')
+                self.freq_scale_factor = assign_frequency_scale_factor(level=freq_level)
+                if self.freq_scale_factor is None:
+                    logger.info(f'Could not determine the harmonic frequencies scaling factor for {freq_level}.')
                     if self.calc_freq_factor:
                         logger.info("Calculating it using Truhlar's method.")
-                        logger.warning("This proceedure normally spawns QM jobs for various small species "
+                        logger.warning("This procedure normally spawns QM jobs for various small species "
                                        "not directly asked for by the user.\n\n")
                         self.freq_scale_factor = determine_scaling_factors(levels=[freq_level],
                                                                            ess_settings=self.ess_settings,
diff --git a/_modules/arc/utils/scale.html b/_modules/arc/utils/scale.html
index 4869aef8a3..1b10c7d353 100644
--- a/_modules/arc/utils/scale.html
+++ b/_modules/arc/utils/scale.html
@@ -386,9 +386,8 @@ 
Source code for arc.utils.scale
 
     with open(info_file_path, 'w') as f:
         f.write(HEADER)
-        database_text = '\n\n\nYou may copy-paste the following harmonic frequency scaling factor(s) to ' \
-                        'the RMG-database repository\n' \
-                        '(under the `freq_dict` in RMG-database/input/quantum_corrections/data.py):\n'
+        database_text = '\n\n\nYou may copy-paste the computed harmonic frequency scaling factor(s) to ARC ' \
+                        '(under the `freq_dict` in ARC/data/freq_scale_factors.yml):\n'
         database_formats = list()
         harmonic_freq_scaling_factors = list()
         for lambda_zpe, level, zpe_dict, execution_time\
@@ -397,13 +396,6 @@ 
Source code for arc.utils.scale
             fundamental_freq_scaling_factor = lambda_zpe * 0.974
             harmonic_freq_scaling_factors.append(fundamental_freq_scaling_factor)
             unconverged = [key for key, val in zpe_dict.items() if val is None]
-            arkane_level = level.to_arkane_level_of_theory().simple()
-            arkane_level_str = f"LevelOfTheory(method='{level.method}'"
-            if arkane_level.basis is not None:
-                arkane_level_str += f",basis='{level.basis}'"
-            if arkane_level.software is not None:
-                arkane_level_str += f",software='{level.software}'"
-            arkane_level_str += f")"
 
             text = f'\n\nLevel of theory: {level}\n'
             if unconverged:
@@ -414,7 +406,7 @@ 
Source code for arc.utils.scale
             text += f'(execution time: {execution_time})\n'
             logger.info(text)
             f.write(text)
-            database_formats.append(f"""             "{arkane_level_str}": {harmonic_freq_scaling_factor:.3f},  # [4]\n""")
+            database_formats.append(f"""  '{level}': {harmonic_freq_scaling_factor:.3f},  # [4]\n""")
         logger.info(database_text)
         f.write(database_text)
         for database_format in database_formats:
diff --git a/api/level.html b/api/level.html
index cafc58889e..e60d99c0c0 100644
--- a/api/level.html
+++ b/api/level.html
@@ -194,7 +194,7 @@
 
A module for working with levels of theory.

 

 

-class arc.level.Level(repr: Optional[Union[str, dict, Level]] = None, method: Optional[str] = None, basis: Optional[str] = None, auxiliary_basis: Optional[str] = None, dispersion: Optional[str] = None, cabs: Optional[str] = None, method_type: Optional[str] = None, software: Optional[str] = None, software_version: Optional[Union[int, float, str]] = None, compatible_ess: Optional[List[str, ...]] = None, solvation_method: Optional[str] = None, solvent: Optional[str] = None, solvation_scheme_level: Optional[Level] = None, args: Optional[Union[Dict[str, str], Iterable, str]] = None)[source]

+class arc.level.Level(repr: Optional[Union[str, dict, Level]] = None, method: Optional[str] = None, basis: Optional[str] = None, auxiliary_basis: Optional[str] = None, dispersion: Optional[str] = None, cabs: Optional[str] = None, method_type: Optional[str] = None, software: Optional[str] = None, software_version: Optional[Union[int, float, str]] = None, compatible_ess: Optional[List[str]] = None, solvation_method: Optional[str] = None, solvent: Optional[str] = None, solvation_scheme_level: Optional[Level] = None, args: Optional[Union[Dict[str, str], Iterable, str]] = None)[source]
 
Uniquely defines the settings used for a quantum calculation level of theory.
 Either repr or method must be specified.

 

@@ -323,6 +323,23 @@
 
 

 
+

+

+arc.level.assign_frequency_scale_factor(level: Union[str, Level]) → Optional[int][source]

+
Assign a frequency scaling factor to a level of theory.

+

+
Parameters:

+
level (Union[str, Level]) – The level of theory.

+

+
Returns:

+
The frequency scaling factor.

+

+
Return type:

+
Optional[int]

+

+

+

+
 

 

 arc.level.get_params_from_arkane_level_of_theory_as_str(arkane_level: str) → Dict[str, str][source]

diff --git a/genindex.html b/genindex.html
index 28673f9a15..6d99127aec 100644
--- a/genindex.html
+++ b/genindex.html
@@ -408,6 +408,8 @@ 
A

         
  • (arc.species.species.TSGuess method)
 
    • 
       
+      
  • assign_frequency_scale_factor() (in module arc.level)
+
    • 
       
  • atom_map (arc.reaction.ARCReaction attribute)
 
       
      
diff --git a/objects.inv b/objects.inv
index c154c8d1ed02edd261cc610a3d14b7f6b0971a0d..589df00e82dfcf0038b312c4c3a2a53645109b6d 100644
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diff --git a/searchindex.js b/searchindex.js
index a0f7c0796b..e2b9e7b660 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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