pyorbb 0.12.7__py3-none-any.whl

pyorbb/__init__.py

@@ -0,0 +1,203 @@
+import os
+import re
+import yaml
+
+from . import orbitals  # noqa
+from .orbitals import Orbitals, MO, FMO  # noqa
+from . import plotting  # noqa
+from . import analysis  # noqa
+from .analysis import Mixer  # noqa
+from . import application  # noqa
+
+if os.path.exists(os.path.join(os.path.split(__file__)[0], 'VERSION')):
+    with open(os.path.join(os.path.split(__file__)[0], 'VERSION')) as version:
+        __version__ = version.read().strip()
+else:
+    __version__ = '0.0.0'
+
+
+
+IRREP_TRANSLATION_LATEX = {
+    "E1:1": r"E$_\mathrm{1}^\mathrm{1}$",
+    "E1:2": r"E$_\mathrm{1}^\mathrm{2}$",
+    "EE1:1": r"E$^{\mathrm{1}\prime}_\mathrm{1}$",
+    "EE1:2": r"E$^{\mathrm{2}\prime}_\mathrm{1}$",
+    "EEE1:1": r"E$^{\mathrm{1}\prime\prime}_\mathrm{1}$",
+    "EEE1:2": r"E$^{\mathrm{2}\prime\prime}_\mathrm{1}$",
+    "AA": r"A$^{\prime}$",
+    "AAA": r"A$^{\prime\prime}$",
+    "AA1": r"A$^{\prime}_\mathrm{1}$",
+    "AA2": r"A$^{\prime}_\mathrm{2}$",
+    "AAA1": r"A$^{\prime\prime}_\mathrm{1}$",
+    "AAA2": r"A$^{\prime\prime}_\mathrm{2}$",
+    "A": r"A",
+    "A1": r"A$_\mathrm{1}$",
+    "A2": r"A$_\mathrm{2}$",
+    "B1": r"B$_\mathrm{1}$",
+    "B2": r"B$_\mathrm{2}$",
+    "T1": r"T$_\mathrm{1}$",
+    "T2": r"T$_\mathrm{2}$",
+    "E": r"E",
+    
+    "SIGMA": r"$\Sigma$",
+    "PI": r"$\Pi$",
+    "DELTA": r"$\Delta$",
+    "PHI": r"$\Phi$",
+
+    "S": r"$s$",
+    "P": r"$p$",
+    "D": r"$d$",
+    "F": r"$f$",
+}
+
+
+IRREP_TRANSLATION_HTML = {
+    "E1": "E<sub>1</sub>",
+    "E1:1": "E<sub>1</sub><sup>1</sup>",
+    "E1:2": "E<sub>1</sub><sup>2</sup>",
+    "EE1": "E<sup>1</sup>′",
+    "EE1:1": "E<sup>1</sup>′<sub>1</sub>",
+    "EE1:2": "E<sup>2</sup>′<sub>1</sub>",
+    "EEE1": "E<sup>1</sup>′′",
+    "EEE1:1": "E<sup>1</sup>′′<sub>1</sub>",
+    "EEE1:2": "E<sup>2</sup>′′<sub>1</sub>",
+    "AA": "A′",
+    "AAA": "A″",
+    "AA1": "A′<sub>1</sub>",
+    "AA2": "A′<sub>2</sub>",
+    "AAA1": "A′′<sub>1</sub>",
+    "AAA2": "A′′<sub>2</sub>",
+    "A": "A",
+    "A1": "A<sub>1</sub>",
+    "A2": "A<sub>2</sub>",
+    "B1": "B<sub>1</sub>",
+    "B2": "B<sub>2</sub>",
+    "T1": "T<sub>1</sub>",
+    "T2": "T<sub>2</sub>",
+    "E": "E",
+    
+    "SIGMA": "<i>σ</i>",
+    "PI": "<i>π</i>",
+    "DELTA": "<i>δ</i>",
+    "PHI": "<i>φ</i>",
+
+    "S": "<i>s</i>",
+    "P": "<i>p</i>",
+    "D": "<i>d</i>",
+    "F": "<i>f</i>",
+}
+
+rcParams_dir = os.path.join(os.path.split(__file__)[0], 'rcParams')
+if os.path.exists(os.path.join(rcParams_dir, 'user.yaml')):
+    rcParams_path = os.path.join(rcParams_dir, 'user.yaml')
+else:
+    rcParams_path = os.path.join(rcParams_dir, 'default.yaml')
+
+with open(rcParams_path) as config:
+    rcParams = yaml.safe_load(config)
+
+
+def save_rcParams():
+    with open(os.path.join(rcParams_dir, 'user.yaml'), 'w+') as user_config:
+        yaml.dump(rcParams, user_config)
+
+
+def reset_rcParams():
+    global rcParams
+
+    with open(os.path.join(rcParams_dir, 'default.yaml')) as config:
+        rcParams = yaml.safe_load(config)
+
+
+def translate_irrep_label(symm_label: str, mode='latex', use_formatting=True) -> str:
+    if mode == 'latex':
+        if symm_label in IRREP_TRANSLATION_LATEX:
+            return IRREP_TRANSLATION_LATEX[symm_label]
+
+        if ':' in symm_label:
+            subspecies, dimension = symm_label.split(':')
+        else:
+            subspecies = symm_label
+            dimension = None
+        
+        if '.' in subspecies:
+            subspecies, parity = subspecies.split('.')
+        else:
+            parity = None
+
+        s = IRREP_TRANSLATION_LATEX.get(subspecies, subspecies)
+        if parity is not None:
+            s += rf'$_\mathrm{{{parity}}}$'
+            
+        if dimension is not None:
+
+            if re.search(r"\d+", dimension): 
+                dimension = re.sub(r"([xyz])(\d+)", r"\1^{\2}", dimension)
+            s += rf'$_{{{dimension}}}$'
+
+        return s
+
+    if mode == 'html':
+        if symm_label in IRREP_TRANSLATION_HTML:
+            s = IRREP_TRANSLATION_HTML[symm_label]
+        else:
+            if ':' in symm_label:
+                subspecies, dimension = symm_label.split(':')
+            else:
+                subspecies = symm_label
+                dimension = None
+            
+            if '.' in subspecies:
+                subspecies, parity = subspecies.split('.')
+            else:
+                parity = None
+
+            s = IRREP_TRANSLATION_HTML.get(subspecies, subspecies)
+            if parity is not None:
+                s += f'<sub>{parity}</sub>'
+            if dimension is not None:
+
+                if re.search(r"\d+", dimension): 
+                    dimension = re.sub(r"([xyz])(\d+)", r"\1<sup>\2</sup>", dimension)
+                s += f'<sub><i>{dimension}</i></sub>'
+
+        if not use_formatting:
+            for format_tag in ['<i>', '</i>', '<sub>', '</sub>', '<sup>', '</sup>']:
+                s = s.replace(format_tag, '')
+
+        return s
+
+    return symm_label
+
+
+def generate_label(orb, mode='latex', include_fragment=False, use_formatting=True):
+    if mode == 'latex':
+        spin_part = {
+            'A': r'$\alpha$',
+            'B': r'$\beta$'
+        }.get(orb.spin, '')
+    elif mode == 'html':
+        spin_part = {
+            'A': '<i>α</i>',
+            'B': '<i>β</i>'
+        }.get(orb.spin, '')
+
+    if isinstance(orb, orbitals.objects.MO):
+        orb_name = f'{orb.name}{spin_part}'
+        orb_name = orb_name.replace(orb.symmetry, translate_irrep_label(orb.symmetry, mode=mode))
+    else:
+        orb_name = orb.name
+        if include_fragment:
+            fragname = orb.fragment
+            orb_name = f'{fragname}({orb_name})'
+        if orb.spin != 'AB':
+            orb_name += spin_part
+
+        orb_name = orb_name.replace(orb.subspecies, translate_irrep_label(orb.subspecies, mode=mode))
+
+    if not use_formatting:
+        for format_tag in ['<i>', '</i>', '<sub>', '</sub>', '<sup>', '</sup>']:
+            orb_name = orb_name.replace(format_tag, '')
+
+    return orb_name
+

pyorbb/__main__.py

@@ -0,0 +1,28 @@
+def main():
+    import platformdirs
+    import os
+    # import contextlib
+    from datetime import datetime
+    import traceback
+    # import faulthandler
+
+    # faulthandler.enable()
+    
+    log_dir = platformdirs.user_log_dir(appname="PyOrbb", appauthor="TheoCheMVU", ensure_exists=True)
+    now = str(datetime.now()).replace(" ", "_").replace(":", "-").split(".")[0]
+    log_file = os.path.join(log_dir, now + ".txt")
+    print("WRITING STDOUT/STDERR TO", log_file)
+    # with open(log_file, "w+") as outp:
+        # with contextlib.redirect_stdout(outp), contextlib.redirect_stderr(outp):
+    try:
+        from pyorbb.application import main
+
+        with main.PyOrbbApp():
+            ...
+
+    except Exception as e:
+        print("".join(traceback.format_exception(type(e), e, e.__traceback__)))
+
+
+if __name__ == '__main__':
+    main()

pyorbb/analysis/__init__.py

@@ -0,0 +1,3 @@
+from . import mixing, movie  # noqa
+from .mixing import Mixer  # noqa
+from .sequential import MOTracker  # noqa