orto 0.27.1__tar.gz → 1.0.1__tar.gz

{orto-0.27.1 → orto-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 0.27.1
+Version: 1.0.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.0.1/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.0.1'

{orto-0.27.1 → orto-1.0.1}/orto/cli.py

@@ -1,23 +1,21 @@
 import argparse
 import xyz_py as xyzp
-import xyz_py.atomic as atomic
-import matplotlib.pyplot as plt
-import matplotlib as mpl
+from xyz_py.atomic import elements as atomic_elements
 import sys
 import pathlib
 import os
 import copy
 import subprocess
-import pandas as pd
+from pandas import read_csv
 import scipy.constants as constants
 import numpy as np
-import extto
-import docx
+from extto import DataNotFoundError
 import re
-import mmap
-import shutil
+from mmap import mmap, ACCESS_READ
+from shutil import move as shutilmove
 
 
+from docx import Document
 from docx.enum.text import WD_ALIGN_PARAGRAPH
 from docx.enum.table import WD_ALIGN_VERTICAL
 from docx.shared import Pt
@@ -28,17 +26,6 @@ from . import job
 from . import utils as ut
 from . import input as inp
 
-# Change matplotlib font size to be larger
-mpl.rcParams.update({'font.size': 12})
-
-# Set user specified font name
-if os.getenv('orto_fontname'):
-    try:
-        plt.rcParams['font.family'] = os.getenv('orto_fontname')
-    except ValueError:
-        ut.cprint('Error in orto_fontname environment variable', 'red')
-        sys.exit(1)
-
 _SHOW_CONV = {
     'on': True,
     'save': False,
@@ -126,7 +113,7 @@ def extract_sf_energies_func(uargs):
         title = 'Spin-Free energies'
 
         # Create document
-        doc = docx.Document()
+        doc = Document()
 
         doc.add_heading(title, 0)
 
@@ -261,7 +248,7 @@ def extract_gmatrix_func(uargs, save=True):
         title = titles[uargs.type]
 
         # Create document
-        doc = docx.Document()
+        doc = Document()
 
         doc.add_heading(title, 0)
 
@@ -357,12 +344,12 @@ def gen_trunc_molden_func(uargs):
     # occurrences of 'Occup='
     _patt = re.compile(b'Sym=')
     with open(uargs.input_file, mode="r") as file_obj:
-        with mmap.mmap(file_obj.fileno(), length=0, access=mmap.ACCESS_READ) as mmap_obj: # noqa
+        with mmap(file_obj.fileno(), length=0, access=ACCESS_READ) as mmap_obj:
             n_MO = len(_patt.findall(mmap_obj))
 
     _patt = re.compile(b'Occup= 0.000000')
     with open(uargs.input_file, mode="r") as file_obj:
-        with mmap.mmap(file_obj.fileno(), length=0, access=mmap.ACCESS_READ) as mmap_obj: # noqa
+        with mmap(file_obj.fileno(), length=0, access=ACCESS_READ) as mmap_obj:
             n_virt = len(_patt.findall(mmap_obj))
 
     ut.cprint(
@@ -399,7 +386,7 @@ def gen_trunc_molden_func(uargs):
     # If no output file given
     if uargs.output_file == '.tmp.molden':
         # Copy new file to original name
-        shutil.move(uargs.output_file, uargs.input_file)
+        shutilmove(uargs.output_file, uargs.input_file)
         uargs.output_file = uargs.input_file
 
     ut.cprint(f'New molden file written to {uargs.output_file}', 'cyan')
@@ -554,6 +541,19 @@ def plot_abs_func(uargs):
     -------
     None
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+
+    # Set user specified font name
+    if os.getenv('orto_fontname'):
+        try:
+            plt.rcParams['font.family'] = os.getenv('orto_fontname')
+        except ValueError:
+            ut.cprint('Error in orto_fontname environment variable', 'red')
+            sys.exit(1)
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
 
     version = oe.OrcaVersionExtractor.extract(uargs.output_file)
 
@@ -744,7 +744,7 @@ def extract_orbs_func(uargs, save=True) -> None:
         # Disable spin if not present in file
         if mult == 1:
             uargs.spin = None
-    except extto.DataNotFoundError:
+    except DataNotFoundError:
         pass
 
     extractors = {
@@ -772,7 +772,7 @@ def extract_orbs_func(uargs, save=True) -> None:
                 )
                 uargs.flavour = name
                 break
-            except extto.DataNotFoundError:
+            except DataNotFoundError:
                 failed += 1
         if failed == len(extractors):
             ut.red_exit(
@@ -783,7 +783,7 @@ def extract_orbs_func(uargs, save=True) -> None:
             data = extractors[uargs.flavour](
                 uargs.output_file
             )
-        except extto.DataNotFoundError as dne:
+        except DataNotFoundError as dne:
             ut.red_exit(str(dne))
 
     # Unpack data
@@ -912,7 +912,7 @@ def extract_freq_func(uargs, save=True):
             data[0]['energy (cm^-1)'][:uargs.num],
             data[0]['IR Intensity (km mol^-1)'][:uargs.num]
         ):
-            print(f'{frq:.2f} {inty:.2f}')
+            print(f'{frq:.5f} {inty:.5f}')
     else:
         # Save to new .csv file
         out_name = f'{uargs.output_file.stem}_frequencies.csv'
@@ -924,7 +924,7 @@ def extract_freq_func(uargs, save=True):
                 data[0]['energy (cm^-1)'][:uargs.num],
                 data[0]['IR Intensity (km mol^-1)'][:uargs.num]
             ):
-                f.write(f'{frq:.2f}, {inty:.2f}\n')
+                f.write(f'{frq:.5f}, {inty:.5f}\n')
 
         ut.cprint(f'Data written to {out_name}', 'cyan')
 
@@ -955,7 +955,7 @@ def extract_pop_func(uargs, save=True) -> None:
             data = oe.MullikenPopulationExtractorDensities.extract(
                 uargs.output_file
             )
-        except extto.DataNotFoundError:
+        except DataNotFoundError:
             data = oe.MullikenPopulationExtractorPopulations.extract(
                 uargs.output_file
             )
@@ -1018,6 +1018,11 @@ def plot_susc_func(uargs) -> None:
         None
 
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
 
     # Extract data from file
     data = oe.SusceptibilityExtractor.extract(uargs.output_file)
@@ -1039,7 +1044,7 @@ def plot_susc_func(uargs) -> None:
 
     # Load experimental data if provided
     if uargs.exp_file is not None:
-        exp_data = pd.read_csv(
+        exp_data = read_csv(
             uargs.exp_file,
             comment='#',
             skipinitialspace=True
@@ -1113,6 +1118,11 @@ def plot_ailft_func(uargs) -> None:
     -------
         None
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
 
     # Create extractor
     data = oe.AILFTOrbEnergyExtractor.extract(uargs.output_file)
@@ -1940,7 +1950,7 @@ def read_args(arg_list=None):
         '-e',
         '--elements',
         type=str,
-        default=atomic.elements,
+        default=atomic_elements,
         nargs='+',
         help='Only print contributions from specified element(s) e.g. Ni'
     )

{orto-0.27.1 → orto-1.0.1}/orto/extractor.py

@@ -538,25 +538,23 @@ class FrequencyExtractor(extto.BetweenExtractor):
         tz_pattern = re.compile(
             r'\([ -]?\d\.\d{6} *-?\d\.\d{6} *(-?\d\.\d{6})\)'
         )
-        # t2_pattern = re.compile(
-        #     r'(\d\.\d{6}) *\([ -]?\d\.\d{6} *-?\d\.\d{6} *-?\d\.\d{6}\)'
-        # )
-        # eps_pat = re.compile(
-        #     r'\d{,4}: * \d{,4}.\d{2} * (\d.\d{6})'
-        # )
+
         tx = np.asarray(
-            [0] * 6 + [float(val) for val in tx_pattern.findall(block)]
+            [float(val) for val in tx_pattern.findall(block)]
         )
         ty = np.asarray(
-            [0] * 6 + [float(val) for val in ty_pattern.findall(block)]
+            [float(val) for val in ty_pattern.findall(block)]
         )
         tz = np.asarray(
-            [0] * 6 + [float(val) for val in tz_pattern.findall(block)]
+            [float(val) for val in tz_pattern.findall(block)]
         )
 
-        # epso = np.asarray(
-        #     [0] * 6 + [float(val) for val in eps_pat.findall(block)]
-        # )
+        # t values are missing for first n_zero modes and for imaginary modes
+        n_missing = len(wavenumbers) - len(tx)
+        z_arr = np.zeros(n_missing)
+        tx = np.concatenate((z_arr, tx))
+        ty = np.concatenate((z_arr, ty))
+        tz = np.concatenate((z_arr, tz))
 
         # This is the T2 printed by ORCA
         # (Dipole derivative wrt to MWC)**2 * vibrational overlap**2
@@ -574,11 +572,10 @@ class FrequencyExtractor(extto.BetweenExtractor):
         icm2eh = 100 / sc.physical_constants['hartree-inverse meter relationship'][0] # noqa
         #
         b2 = np.zeros_like(wavenumbers)
-        n_zero = np.where(wavenumbers > 1E-4)[0][0]
-        b2[n_zero:] = 1 / (2 * icm2eh * wavenumbers[n_zero:])
+        b2[n_missing:] = 1 / (2 * icm2eh * wavenumbers[n_missing:])
         # divide by sqrt(b2)
         # to give units of e m_e^-1/2
-        t[n_zero:] /= np.sqrt(b2[n_zero:])
+        t[n_missing:] /= np.sqrt(b2[n_missing:])
 
         # Convert to SI
         # First convert electrons to coulombs
@@ -588,12 +585,13 @@ class FrequencyExtractor(extto.BetweenExtractor):
         t *= (sc.m_e)**-0.5
 
         # Calculate A_e in units of m mol^-1
+        # this is "Intensity" in Orca
         ae = np.ones_like(wavenumbers)
-        ae[:n_zero] = 0
+        ae[:n_missing] = 0
         ae *= sc.Avogadro / (12 * sc.epsilon_0 * sc.speed_of_light**2)
-        ae[n_zero:] *= t[n_zero:] ** 2
+        ae[n_missing:] *= t[n_missing:] ** 2
         # and convert to km mol^-1
-        ae[n_zero:] /= 1000
+        ae[n_missing:] /= 1000
 
         # Convert absorbance to linear
         alin = ae / np.log(10)

{orto-0.27.1 → orto-1.0.1}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 0.27.1
+Version: 1.0.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-0.27.1 → orto-1.0.1}/setup.py

@@ -8,7 +8,7 @@ Please see the `orto` documentation for more details.
 
 # DO NOT EDIT THIS NUMBER!
 # IT IS AUTOMATICALLY CHANGED BY python-semantic-release
-__version__ = '0.27.1'
+__version__ = '1.0.1'
 
 setuptools.setup(
     name='orto',

orto-0.27.1/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '0.27.1'