orto 1.0.0__tar.gz → 1.0.2__tar.gz

{orto-1.0.0 → orto-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.0.0
+Version: 1.0.2
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.0.2/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.0.2'

{orto-1.0.0 → orto-1.0.2}/orto/cli.py

@@ -1,43 +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
-import scipy.constants as constants
+import csv
 import numpy as np
-import extto
-import docx
 import re
-import mmap
-import shutil
+from mmap import mmap, ACCESS_READ
+from shutil import move as shutilmove
 
-
-from docx.enum.text import WD_ALIGN_PARAGRAPH
-from docx.enum.table import WD_ALIGN_VERTICAL
-from docx.shared import Pt
-
-from . import plotter
-from . import extractor as oe
 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)
+from . import constants as cst
+from .exceptions import DataNotFoundError, DataFormattingError
 
 _SHOW_CONV = {
     'on': True,
@@ -69,6 +47,7 @@ def extract_coords_func(uargs, save=True):
     -------
         None
     '''
+    from . import extractor as oe
 
     # Open file and extract coordinates
     labels, coords = oe.get_coords(
@@ -96,6 +75,11 @@ def extract_sf_energies_func(uargs):
     '''
     Wrapper for cli call to extract spin-free energies
     '''
+    from . import extractor as oe
+    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
 
     all_data = oe.SpinFreeEnergyExtractor().extract(
         uargs.output_file
@@ -126,7 +110,7 @@ def extract_sf_energies_func(uargs):
         title = 'Spin-Free energies'
 
         # Create document
-        doc = docx.Document()
+        doc = Document()
 
         doc.add_heading(title, 0)
 
@@ -179,6 +163,7 @@ def extract_so_energies_func(uargs):
     '''
     Wrapper for cli call to extract spin-orbit energies
     '''
+    from . import extractor as oe
 
     all_energies = oe.SpinOrbitEnergyExtractor().extract(
         uargs.output_file
@@ -219,6 +204,11 @@ def extract_gmatrix_func(uargs, save=True):
     -------
         None
     '''
+    from . import extractor as oe
+    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
 
     choices = {
         'total': oe.GMatrixExtractor,
@@ -261,7 +251,7 @@ 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 +347,12 @@ 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 +389,7 @@ 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')
@@ -420,6 +410,7 @@ def gen_job_func(uargs):
     -------
     None
     '''
+    from . import input as inp
 
     for input_file in uargs.input_files:
 
@@ -474,13 +465,13 @@ def gen_job_func(uargs):
         # Check xyz file is present
         try:
             inp.check_xyz(oj.input_file, uargs.skip_xyz)
-        except (oe.DataNotFoundError, oe.DataFormattingError) as e:
+        except (DataNotFoundError, DataFormattingError) as e:
             ut.red_exit(str(e))
 
         # Check for moread and moinp
         try:
             inp.check_moinp_moread(oj.input_file)
-        except (oe.DataNotFoundError, oe.DataFormattingError) as e:
+        except (DataNotFoundError, DataFormattingError) as e:
             ut.red_exit(str(e))
 
         # Submitter configuration options
@@ -491,7 +482,7 @@ def gen_job_func(uargs):
         try:
             n_procs = inp.get_nprocs(oj.input_file)
             maxcore = inp.get_maxcore(oj.input_file)
-        except (oe.DataNotFoundError, oe.DataFormattingError) as e:
+        except (DataNotFoundError, DataFormattingError) as e:
             ut.red_exit(str(e))
 
         # If memory and procs specified as arguments, give warning when
@@ -554,6 +545,21 @@ def plot_abs_func(uargs):
     -------
     None
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+    from . import plotter
+    from . import extractor as oe
+
+    # 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)
 
@@ -655,6 +661,21 @@ def plot_ir_func(uargs):
     -------
     None
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+    from . import plotter
+    from . import extractor as oe
+
+    # 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})
 
     # Extract frequency information
     data = oe.FrequencyExtractor.extract(uargs.output_file)
@@ -665,7 +686,7 @@ def plot_ir_func(uargs):
     data = data[0]
 
     # Plot infrared spectrum
-    fig, ax = plotter.plot_ir(
+    plotter.plot_ir(
         data['energy (cm^-1)'],
         data['epsilon (L mol^-1 cm^-1)'],
         linewidth=uargs.linewidth,
@@ -691,6 +712,7 @@ def distort_func(uargs):
         None
 
     '''
+    from . import extractor as oe
 
     # Open file and extract coordinates
     labels, coords = oe.get_coords(
@@ -737,6 +759,7 @@ def extract_orbs_func(uargs, save=True) -> None:
     -------
         None
     '''
+    from . import extractor as oe
 
     # Check for spin in file, if present
     try:
@@ -744,7 +767,7 @@ 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 +795,7 @@ 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 +806,7 @@ 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
@@ -896,6 +919,7 @@ def extract_freq_func(uargs, save=True):
     -------
         None
     '''
+    from . import extractor as oe
 
     # Extract frequency information
     data = oe.FrequencyExtractor.extract(uargs.output_file)
@@ -945,6 +969,7 @@ def extract_pop_func(uargs, save=True) -> None:
     -------
         None
     '''
+    from . import extractor as oe
 
     if uargs.flavour in ['loewdin', 'lowdin']:
         data = oe.LoewdinPopulationExtractor.extract(
@@ -955,7 +980,7 @@ 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 +1043,13 @@ def plot_susc_func(uargs) -> None:
         None
 
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+    from . import plotter
+    from . import extractor as oe
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
 
     # Extract data from file
     data = oe.SusceptibilityExtractor.extract(uargs.output_file)
@@ -1037,22 +1069,28 @@ def plot_susc_func(uargs) -> None:
             'green'
         )
 
-    # Load experimental data if provided
     if uargs.exp_file is not None:
-        exp_data = pd.read_csv(
-            uargs.exp_file,
-            comment='#',
-            skipinitialspace=True
-        )
+        exp_data = {'Temperature (K)': [], 'chi*T (cm3*K/mol)': []}
+        with open(uargs.exp_file, newline='') as csvfile:
+            reader = csv.DictReader(
+                row for row in csvfile if not row.startswith('#')
+            )
+            for row in reader:
+                exp_data['Temperature (K)'].append(
+                    float(row['Temperature (K)'])
+                )
+                exp_data['chi*T (cm3*K/mol)'].append(
+                    float(row['chi*T (cm3*K/mol)'])
+                )
 
     # Conversion factors from cm3 K mol^-1 to ...
     convs = {
-        'A3 K': 1E24 / constants.Avogadro,
+        'A3 K': 1E24 / cst.AVOGADRO,
         'A3 mol-1 K': 1E24,
-        'cm3 K': 1 / constants.Avogadro,
+        'cm3 K': 1 / cst.AVOGADRO,
         'cm3 mol-1 K': 1,
-        'emu K': 1 / (4 * constants.pi * constants.Avogadro),
-        'emu mol-1 K': 1 / (4 * constants.pi)
+        'emu K': 1 / (4 * np.pi * cst.AVOGADRO),
+        'emu mol-1 K': 1 / (4 * np.pi)
     }
 
     unit_labels = {
@@ -1078,7 +1116,10 @@ def plot_susc_func(uargs) -> None:
         if uargs.exp_file is not None:
             ax.plot(
                 exp_data['Temperature (K)'],
-                exp_data['chi*T (cm3*K/mol)'] * convs[uargs.esusc_units],
+                [
+                    val * convs[uargs.esusc_units]
+                    for val in exp_data['chi*T (cm3*K/mol)']
+                ],
                 lw=0,
                 marker='o',
                 fillstyle='none',
@@ -1113,6 +1154,13 @@ def plot_ailft_func(uargs) -> None:
     -------
         None
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+    from . import plotter
+    from . import extractor as oe
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
 
     # Create extractor
     data = oe.AILFTOrbEnergyExtractor.extract(uargs.output_file)
@@ -1940,7 +1988,7 @@ 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-1.0.2/orto/constants.py

@@ -0,0 +1,8 @@
+AVOGADRO = 6.02214076e23  # mol^-1
+HARTREE2INVERSE_M = 2.194746313705E7  # m^-1
+HARTREE2INVERSE_CM = 100 / HARTREE2INVERSE_M
+ELECTRON_CHARGE = 1.602176487e-19  # C
+ELECTRON_MASS = 9.10938215E-31  # kg
+EPSILON_0 = 8.8541878128E-12  # F m^-1
+SPEED_OF_LIGHT_M_S = 299792458.0  # m s^-1
+SPEED_OF_LIGHT_CM_S = SPEED_OF_LIGHT_M_S * 100.0  # cm s^-1

orto-1.0.2/orto/exceptions.py

@@ -0,0 +1,5 @@
+from extto import DataNotFoundError as exttoDNF
+from extto import DataFormattingError as exttoDFE
+
+DataNotFoundError = exttoDNF
+DataFormattingError = exttoDFE

{orto-1.0.0 → orto-1.0.2}/orto/extractor.py

@@ -7,12 +7,10 @@ import re
 import pandas as pd
 from io import StringIO
 import pathlib
-import scipy.constants as sc
 import copy
 
-# Reimplemented for convenience
-DataNotFoundError = extto.DataNotFoundError
-DataFormattingError = extto.DataFormattingError
+from .exceptions import DataFormattingError
+from . import constants as const
 
 
 class OrcaVersionExtractor(extto.LineExtractor):
@@ -569,26 +567,24 @@ class FrequencyExtractor(extto.BetweenExtractor):
         # in atomic units
         # b^2 = hbar/(2*c*nubar) --> 1/(2*nubar)
         # m_e^-1/2 a_0
-        icm2eh = 100 / sc.physical_constants['hartree-inverse meter relationship'][0] # noqa
-        #
         b2 = np.zeros_like(wavenumbers)
-        b2[n_missing:] = 1 / (2 * icm2eh * wavenumbers[n_missing:])
+        b2[n_missing:] = 1 / (2 * const.HARTREE2INVERSE_CM * wavenumbers[n_missing:]) # noqa
         # divide by sqrt(b2)
         # to give units of e m_e^-1/2
         t[n_missing:] /= np.sqrt(b2[n_missing:])
 
         # Convert to SI
         # First convert electrons to coulombs
-        t *= sc.e
+        t *= const.ELECTRON_CHARGE
 
         # and then reciprocal atomic mass units (m_e^-1/2) to kg^-1/2
-        t *= (sc.m_e)**-0.5
+        t *= (const.ELECTRON_MASS)**-0.5
 
         # Calculate A_e in units of m mol^-1
         # this is "Intensity" in Orca
         ae = np.ones_like(wavenumbers)
         ae[:n_missing] = 0
-        ae *= sc.Avogadro / (12 * sc.epsilon_0 * sc.speed_of_light**2)
+        ae *= const.AVOGADRO / (12 * const.EPSILON_0 * const.SPEED_OF_LIGHT_M_S**2) # noqa
         ae[n_missing:] *= t[n_missing:] ** 2
         # and convert to km mol^-1
         ae[n_missing:] /= 1000

{orto-1.0.0 → orto-1.0.2}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.0.0
+Version: 1.0.2
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.0.0 → orto-1.0.2}/orto.egg-info/SOURCES.txt

@@ -4,6 +4,8 @@ setup.py
 ./orto/__init__.py
 ./orto/__version__.py
 ./orto/cli.py
+./orto/constants.py
+./orto/exceptions.py
 ./orto/extractor.py
 ./orto/input.py
 ./orto/job.py
@@ -12,6 +14,8 @@ setup.py
 orto/__init__.py
 orto/__version__.py
 orto/cli.py
+orto/constants.py
+orto/exceptions.py
 orto/extractor.py
 orto/input.py
 orto/job.py

{orto-1.0.0 → orto-1.0.2}/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__ = '1.0.0'
+__version__ = '1.0.2'
 
 setuptools.setup(
     name='orto',

orto-1.0.0/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.0.0'