orto 1.0.1__py3-none-any.whl → 1.0.3__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.0.1'
+__version__ = '1.0.3'

orto/cli.py

@@ -6,25 +6,16 @@ import pathlib
 import os
 import copy
 import subprocess
-from pandas import read_csv
-import scipy.constants as constants
+import csv
 import numpy as np
-from extto import DataNotFoundError
 import re
 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
-
-from . import plotter
-from . import extractor as oe
 from . import job
 from . import utils as ut
-from . import input as inp
+from . import constants as cst
+from .exceptions import DataNotFoundError, DataFormattingError
 
 _SHOW_CONV = {
     'on': True,
@@ -56,6 +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(
@@ -83,6 +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
@@ -166,6 +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
@@ -206,6 +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,
@@ -407,6 +410,7 @@ def gen_job_func(uargs):
     -------
     None
     '''
+    from . import input as inp
 
     for input_file in uargs.input_files:
 
@@ -461,13 +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
@@ -478,7 +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
@@ -543,6 +547,8 @@ def plot_abs_func(uargs):
     '''
     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'):
@@ -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:
@@ -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(
@@ -1020,6 +1045,8 @@ def plot_susc_func(uargs) -> 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})
@@ -1042,22 +1069,28 @@ def plot_susc_func(uargs) -> None:
             'green'
         )
 
-    # Load experimental data if provided
     if uargs.exp_file is not None:
-        exp_data = 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 = {
@@ -1083,7 +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',
@@ -1120,6 +1156,8 @@ def plot_ailft_func(uargs) -> 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})

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/exceptions.py

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

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/input.py

@@ -4,6 +4,7 @@ import numpy as np
 import copy
 import xyz_py as xyzp
 
+from .exceptions import DataNotFoundError, DataFormattingError
 from . import extractor as oe
 from . import utils as ut
 
@@ -25,20 +26,20 @@ def get_nprocs(file_name: str | Path) -> int:
 
     Raises
     ------
-    oe.DataNotFoundError
+    DataNotFoundError
         If neither the PAL nor NProcs keyword is present in the input file
-    oe.DataFormattingError
+    DataFormattingError
         If both PAL and NProcs are present in the input file
-    oe.DataFormattingError
+    DataFormattingError
         If the PAL keyword is not a power of 2
-    oe.DataFormattingError
+    DataFormattingError
         If the %PAL block is malformed
     '''
 
     # Check for simple input line beginning with !
     try:
         simple = oe.SimpleInputExtractor.extract(file_name)
-    except oe.DataNotFoundError:
+    except DataNotFoundError:
         ut.red_exit(
             'Error: Missing simple input line (or !) in input file'
         )
@@ -66,22 +67,22 @@ def get_nprocs(file_name: str | Path) -> int:
     # Check for %PAL block in input file
     try:
         n_procs = oe.NProcsInputExtractor.extract(file_name)[0]
-    except oe.DataNotFoundError:
+    except DataNotFoundError:
         if _palprocs:
             n_procs = copy.copy(_palprocs)
             _palprocs = 0
         else:
-            raise oe.DataNotFoundError(
+            raise DataNotFoundError(
                 f'Missing number of processors in {file_name}\n'
                 'e.g. %pal nprocs 16 end'
             )
-    except oe.DataFormattingError:
-        raise oe.DataFormattingError(
+    except DataFormattingError:
+        raise DataFormattingError(
             f'%PAL block is malformed, perhaps missing END?\n in {file_name}'
         )
 
     if n_procs and _palprocs:
-        raise oe.DataFormattingError(
+        raise DataFormattingError(
             'Error: Both PAL and NProcs found in input file\n'
             f'PAL: {_palprocs}, NProcs: {n_procs}'
         )
@@ -107,15 +108,15 @@ def get_maxcore(file_name: str | Path) -> int:
 
     Raises
     ------
-    oe.DataNotFoundError
+    DataNotFoundError
         If %maxcore is not present in the input file
     '''
 
     # Load max core memory from input file
     try:
         maxcore = oe.MaxCoreInputExtractor.extract(file_name)[0]
-    except oe.DataNotFoundError:
-        raise oe.DataNotFoundError(
+    except DataNotFoundError:
+        raise DataNotFoundError(
             f'Missing max core memory in {file_name}\n'
             'e.g. %maxcore 3000'
         )
@@ -142,21 +143,21 @@ def check_xyz(file_name: str | Path, skip_check) -> None:
 
     Raises
     ------
-    oe.DataNotFoundError
+    DataNotFoundError
         If neither *xyzfile nor *xyz are present in the input file
-    oe.DataFormattingError
+    DataFormattingError
         If xyz file is not formatted correctly
     '''
 
     # Get xyz file name and check it exists and is formatted correctly
     try:
         xyz_file = oe.XYZFileInputExtractor.extract(file_name)
-    except oe.DataNotFoundError:
+    except DataNotFoundError:
         xyz_file = []
 
     try:
         xyzline = oe.XYZInputExtractor.extract(file_name)
-    except oe.DataNotFoundError:
+    except DataNotFoundError:
         xyzline = []
 
     if not len(xyz_file) and not len(xyzline):
@@ -183,7 +184,7 @@ def check_xyz(file_name: str | Path, skip_check) -> None:
                     allow_indices=False
                 )
             except xyzp.XYZError as e:
-                raise oe.DataFormattingError(
+                raise DataFormattingError(
                     f'{e}\n Use -sx to skip this check at your peril'
                 )
     return
@@ -207,31 +208,31 @@ def check_moinp_moread(file_name: str | Path) -> None:
 
     Raises
     ------
-    oe.DataNotFoundError
+    DataNotFoundError
         If only one of MORead and MOInp are present in the input file
-    oe.DataFormattingError
+    DataFormattingError
         If the stem of the input file and MOInp file are the same
-    oe.DataNotFoundError
+    DataNotFoundError
         If the MOInp file cannot be found
-    oe.DataFormattingError
+    DataFormattingError
         If the MOInp file has no extension
     '''
 
     # Check if MORead and/or MOInp are present
     try:
         moread = oe.MOReadExtractor.extract(file_name)
-    except oe.DataNotFoundError:
+    except DataNotFoundError:
         moread = []
     try:
         moinp = oe.MOInpExtractor.extract(file_name)
-    except oe.DataNotFoundError:
+    except DataNotFoundError:
         moinp = []
 
     # Error if only one word present or if more than one of each word
     if len(moinp) ^ len(moread):
-        raise oe.DataFormattingError('Error: Missing one of MOInp or MORead')
+        raise DataFormattingError('Error: Missing one of MOInp or MORead')
     if len(moinp) + len(moread) > 2:
-        raise oe.DataFormattingError(
+        raise DataFormattingError(
             'Error: Multiple MORead and/or MOInp detected'
         )
 
@@ -239,17 +240,17 @@ def check_moinp_moread(file_name: str | Path) -> None:
         # Error if input orbitals have same stem as input file
         moinp = Path(moinp[0])
         if moinp.stem == file_name.stem:
-            raise oe.DataFormattingError(
+            raise DataFormattingError(
                 'Error: Stem of orbital and input files cannot match'
             )
 
         # Error if cannot find orbital file
         if not moinp.suffix:
-            raise oe.DataFormattingError(
+            raise DataFormattingError(
                 f'Error: Orbital file {moinp} has no extension'
             )
         if not moinp.exists():
-            raise oe.DataFormattingError(
+            raise DataFormattingError(
                 f'Error: Orbital file {moinp} cannot be found'
             )
 

{orto-1.0.1.dist-info → orto-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.0.1
+Version: 1.0.3
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.0.3.dist-info/RECORD

@@ -0,0 +1,15 @@
+orto/__init__.py,sha256=iSR4TAfpJn1_mwTnnncgwmWBz3q_ImdmhnOORKcOvE0,63
+orto/__version__.py,sha256=qKK4BMzdt84HiCorJPWqgEfa_DbJeuGx_bIPrDui2vc,22
+orto/cli.py,sha256=yckaw1kryADOWz-NZPzXpXYTp8L9X89TVqUErfg3RsY,61241
+orto/constants.py,sha256=2obWYg306Lce4U9Qs4MHg1yZq7SHFkazG-cnkD5svpo,343
+orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
+orto/extractor.py,sha256=tO2oFf6Cgwdnh_m1v8r1rXQO2_FL7s-1KBqLPy6zNco,67384
+orto/input.py,sha256=cVhApyjCbqIDA0uRGqmt3UwKEn7djPjSWob70Ghg9fw,7060
+orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
+orto/plotter.py,sha256=ICrO03T_HGe-H1XKZ2qzsKYdPY44E0PKiXqIQQawd7I,15633
+orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
+orto-1.0.3.dist-info/METADATA,sha256=JaD-1F-ZVeHqy8bNgnNiRjweFaREtA3t-JPk8o1hixY,1140
+orto-1.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.0.3.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.0.3.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.0.3.dist-info/RECORD,,

orto-1.0.1.dist-info/RECORD

@@ -1,13 +0,0 @@
-orto/__init__.py,sha256=iSR4TAfpJn1_mwTnnncgwmWBz3q_ImdmhnOORKcOvE0,63
-orto/__version__.py,sha256=3KXfAcA5rzzQXMtfwpHphgbJNZdA0XWaW96kdWVSZJw,22
-orto/cli.py,sha256=xRcJw_65gQmpBsmruRe46r2gd7fBdLpoh9Z0oPLPcM8,59795
-orto/extractor.py,sha256=kJnVI_Zwz7yorbojWdgxN-NSspJIY9pKoDb1RD2dHUg,67488
-orto/input.py,sha256=UMYNPGeqOCNKvPYJVfVS2JU7Ost_xM1ZG28t5f9-Er0,7084
-orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
-orto/plotter.py,sha256=ICrO03T_HGe-H1XKZ2qzsKYdPY44E0PKiXqIQQawd7I,15633
-orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
-orto-1.0.1.dist-info/METADATA,sha256=tkPj-dCGN-DhaYdlyGkXVysH-4STdCAf4kPr-hXYbfU,1140
-orto-1.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orto-1.0.1.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
-orto-1.0.1.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
-orto-1.0.1.dist-info/RECORD,,