orto 1.12.0__py3-none-any.whl → 1.13.1__py3-none-any.whl

orto/plotter.py

@@ -1,5 +1,4 @@
 import matplotlib.pyplot as plt
-import matplotlib as mpl
 from matplotlib.ticker import AutoMinorLocator
 import numpy as np
 from numpy.typing import ArrayLike
@@ -10,11 +9,50 @@ from . import utils as ut
 from . import data
 
 
+def set_axlims(ax: plt.Axes, type: str, limits: list[float | str]) -> None:
+    '''
+    Sets axis limits of specified axis given a set of limit\n
+    values or string 'auto'
+    '''
+
+    if type == 'y':
+        gmethod = ax.get_ylim
+        smethod = ax.set_ylim
+    elif type == 'x':
+        gmethod = ax.get_xlim
+        smethod = ax.set_xlim
+    else:
+        raise ValueError(f'Unknown axis type {type}')
+
+    _limits = limits.copy()
+    if _limits[0] != _limits[1]:
+        # Lower limit either auto or specified
+        if isinstance(_limits[0], str):
+            if _limits[0] == 'auto':
+                _limits[0] = gmethod()[0]
+            elif ut.is_floatable(_limits[0]):
+                _limits[0] = float(_limits[0])
+            else:
+                raise ValueError(f'Invalid {type} limit value: {_limits[0]}')
+        # Upper limit either auto or specified
+        if isinstance(_limits[1], str):
+            if _limits[1] == 'auto':
+                _limits[1] = gmethod()[1]
+            elif ut.is_floatable(_limits[1]):
+                _limits[1] = float(_limits[1])
+            else:
+                raise ValueError(f'Invalid {type} limit value: {_limits[1]}')
+        # Set values
+        smethod([_limits[0], _limits[1]])
+
+    return
+
+
 def plot_absorption_spectrum(abs_data: data.AbsorptionData,
                              linecolor: str = 'black',
-                             stickcolour: str = 'black',
-                             x_lim: list[float] = ['auto', 'auto'],
-                             y_lim: list[float] = [0., 'auto'],
+                             stickcolor: str = 'black',
+                             xlim: list[float] = ['auto', 'auto'],
+                             ylim: list[float] = [0., 'auto'],
                              x_shift: float = 0.,
                              normalise: bool = False,
                              osc_style: str = 'separate',
@@ -26,7 +64,7 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
                              window_title: str = 'Absorption Spectrum',
                              legend: bool = True) -> tuple[plt.Figure, plt.Axes, plt.Axes | None]: # noqa
     '''
-    Plots absorption spectrum from AbsorptionSpectrum object.\n
+    Plots an absorption spectrum from AbsorptionSpectrum object.\n
 
     Parameters
     ----------
@@ -34,11 +72,11 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
         Data object containing absorption data and spectrum
     linecolor: str, default 'black'
         Color of the continuous spectrum line
-    stickcolour: str, default 'black'
+    stickcolor: str, default 'black'
         Color of the oscillator strength sticks
-    x_lim: list[float], default ['auto', 'auto']
+    xlim: list[float], default ['auto', 'auto']
         Minimum and maximum x-values to plot
-    y_lim: list[float | str], default [0., 'auto']
+    ylim: list[float | str], default [0., 'auto']
         Minimum and maximum y-values to plot
     normalise: bool, default False
         If True, normalise the absorption spectrum to the maximum value.
@@ -61,7 +99,7 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
         If True, plot is shown on screen
     verbose: bool, default True
         If True, plot file location is written to terminal
-    window_title: str, default 'UV-Visible Absorption Spectrum'
+    window_title: str, default 'Absorption Spectrum'
         Title of figure window, not of plot
     legend: bool, default True
         If True, a legend is added to the plot
@@ -95,27 +133,11 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
     if oax is None and osc_style == 'separate':
         oax = ax.twinx()
 
-    if not isinstance(x_lim, list):
-        raise ValueError('`x_lim` must be a list of values')
+    if not isinstance(xlim, list):
+        raise ValueError('`xlim` must be a list of values')
 
-    if x_lim[0] != x_lim[1]:
-        if isinstance(x_lim[0], str):
-            if x_lim[0] == 'auto':
-                x_lim[0] = ax.get_ylim()[0]
-            elif ut.is_floatable(x_lim[0]):
-                x_lim[0] = float(x_lim[0])
-            else:
-                raise ValueError(f'Invalid x_lim[0] value: {x_lim[0]}')
-        if isinstance(x_lim[1], str):
-            if x_lim[1] == 'auto':
-                x_lim[1] = ax.get_ylim()[1]
-            elif ut.is_floatable(x_lim[1]):
-                x_lim[1] = float(x_lim[1])
-            else:
-                raise ValueError(f'Invalid x_lim[1] value: {x_lim[1]}')
-
-    # Set limits and range of continuous variable
-    # ax.set_xlim([x_lim[0], x_lim[1]])
+    # Set x limits if specified
+    set_axlims(ax, 'x', xlim)
 
     # Normalisation of spectrum
     if normalise:
@@ -165,7 +187,7 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
             _osc,
             basefmt=' ',
             markerfmt=' ',
-            linefmt=stickcolour
+            linefmt=stickcolor
         )
         plt.setp(stemlines, 'linewidth', 1.1)
         oax.yaxis.set_minor_locator(AutoMinorLocator())
@@ -180,7 +202,7 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
             abs_data.osc_strengths/np.max(abs_data.osc_strengths) * np.max(_y_values), # noqa
             basefmt=' ',
             markerfmt=' ',
-            linefmt=stickcolour
+            linefmt=stickcolor
         )
         oax.set_yticks([])
         oax.spines['right'].set_visible(False)
@@ -197,22 +219,7 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
         ax.spines['top'].set_visible(False)
 
     # Set y limits if specified
-    _y_lim = y_lim.copy()
-    if _y_lim[0] != _y_lim[1]:
-        # Lower limit either auto or specified
-        if isinstance(_y_lim[0], str):
-            if _y_lim[0] == 'auto':
-                _y_lim[0] = ax.get_ylim()[0]
-            else:
-                _y_lim[0] = float(_y_lim[0])
-        # Upper limit either auto or specified
-        if isinstance(_y_lim[1], str):
-            if _y_lim[1] == 'auto':
-                _y_lim[1] = ax.get_ylim()[1]
-            else:
-                _y_lim[1] = float(_y_lim[1])
-        # Set values
-        ax.set_ylim([_y_lim[0], _y_lim[1]])
+    set_axlims(ax, 'y', ylim)
 
     ax.xaxis.set_minor_locator(AutoMinorLocator())
     ax.yaxis.set_minor_locator(AutoMinorLocator())
@@ -242,74 +249,106 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
     return fig, ax, oax
 
 
-def wl_to_wn(wl: float) -> float:
-    if wl == 0:
-        return 0.
-    else:
-        return 1E7 / wl
-
-
-def plot_chit(chit: ArrayLike, temps: ArrayLike, fields: ArrayLike = None,
-              y_unit: str = r'cm^3\,K\,mol^{-1}', # noqa
-              save: bool = False, save_name: str = 'chit_vs_t.png',
-              show: bool = False, window_title: str = 'Calculated Susceptibility') -> tuple[plt.Figure, plt.Axes]: # noqa
-    r'''
-    Plots susceptibility*T data as a function of temperature
+def plot_susceptibility(susc_data: data.SuscseptibilityData,
+                        y_style: str = 'XT',
+                        label: str = None,
+                        linecolor: str = 'black',
+                        xlim: list[float] = ['auto', 'auto'],
+                        ylim: list[float] = [0., 'auto'],
+                        fig: plt.Figure = None, ax: plt.Axes = None,
+                        save: bool = False,
+                        save_name: str = 'magnetic_susceptibility.png',
+                        show: bool = False,
+                        verbose: bool = True,
+                        window_title: str = 'Magnetic Susceptibility',
+                        legend: bool = True) -> tuple[plt.Figure, plt.Axes]:
+    '''
+    Plots magnetic susceptibility data from SusceptibilityData object
 
     Parameters
     ----------
-    chit: array_like
-        Susceptibility * Temperature
-    temps: array_like
-        Temperatures in Kelvin
-    fields: array_like, optional
-        If specified, splits data according to applied magnetic field.\n
-        One plot, with one trace per field.
-    y_unit: str, default 'cm^3\ K\ mol^{-1}'
-        Mathmode y-unit which matches input chit data
+    susc_data: data.SusceptibilityData
+        Data object containing susceptibility data
+    y_style: str, default 'XT'
+        Quanity to plot on y axis, one of\n
+        'XT': chi*T\n
+        'X': chi\n
+        '1/X': 1/chi
+    label: str
+        Label for this trace used in legend
+    linecolor: str, default 'black'
+        Color of the data line
+    xlim: list[float], default ['auto', 'auto']
+        Minimum and maximum x-values to plot
+    ylim: list[float | str], default [0., 'auto']
+        Minimum and maximum y-values to plot
+    fig: plt.Figure | None, optional
+        If provided, uses this Figure object for plotting
+    ax: plt.Axes | None, optional
+        If provided, plots data to this axis
     save: bool, default False
         If True, plot is saved to save_name
-    save_name: str, default 'chit_vs_t.png'
+    save_name: str | pathlib.Path, default 'magnetic_susceptibility.png'
         If save is True, plot is saved to this location/filename
     show: bool, default False
         If True, plot is shown on screen
-    window_title: str, default 'Calculated Susceptibility'
+    verbose: bool, default True
+        If True, plot file location is written to terminal
+    window_title: str, default 'Magnetic Susceptibility'
         Title of figure window, not of plot
+    legend: bool, default True
+        If True, a legend is added to the plot
+
     Returns
     -------
     plt.Figure
-        Matplotlib Figure objectwidth
+        Matplotlib Figure object
     plt.Axes
-        Matplotlib Axis object for plot
-    ''' # noqa
-
-    # Create figure and axes
-    fig, ax = plt.subplots(
-        1,
-        1,
-        figsize=(4 * (1 + np.sqrt(5))/2, 4),
-        num=window_title
-    )
+        Matplotlib Axis object for main plot
+    '''
+
+    save_name = pathlib.Path(save_name)
 
-    if fields is None:
-        # Plot data as it is
-        ax.plot(temps, chit, color='k', label='Calculated')
+    if fig is None or ax is None:
+        width = 4
+        width_cm = 10.4
+        golden = (1 + np.sqrt(5))/2
+        fig, ax = plt.subplots(
+            1,
+            1,
+            num=window_title,
+            figsize=(width, width / golden)
+        )
     else:
-        # Split data by field
-        ufields = np.unique(fields)
-
-        for ufield in ufields:
-            _temp = temps[fields == ufield]
-            _chit = chit[fields == ufield]
-            ax.plot(
-                _temp,
-                _chit,
-                label=f'Calculated ($H$ = {ufield:.1f} Oe)'
-            )
-        ax.legend(frameon=False)
+        width = fig.get_size_inches()[0]
+        width_cm = width * 2.54
+
+    if y_style == 'XT':
+        y_data = susc_data.chis * susc_data.temperatures
+    elif y_style == 'X':
+        y_data = susc_data.chis
+    elif y_style == '1/X':
+        y_data = 1 / susc_data.chis
+    else:
+        raise ValueError(f'Unknown y_style {y_style}')
+
+    if label is None:
+        label = f'Calculated ($H$ = {susc_data.field:.1f} Oe)'
+
+    ax.plot(
+        susc_data.temperatures,
+        y_data,
+        label=label,
+        lw=1.5,
+        color=linecolor
+    )
+
+    # Set x and y limits
+    set_axlims(ax, 'x', xlim)
+    set_axlims(ax, 'y', ylim)
 
     ax.set_xlabel('$T$ (K)')
-    ax.set_ylabel(rf'$\chi T\,\mathregular{{({y_unit})}}$')
+    ax.set_ylabel(r'$\chi T\,\mathregular{cm^3\,K\,mol^{-1}}$')
 
     ax.xaxis.set_minor_locator(AutoMinorLocator())
     ax.yaxis.set_minor_locator(AutoMinorLocator())
@@ -318,6 +357,15 @@ def plot_chit(chit: ArrayLike, temps: ArrayLike, fields: ArrayLike = None,
 
     if save:
         plt.savefig(save_name, dpi=500)
+        if verbose:
+            ut.cprint(
+                f'\nSpectrum saved to\n {save_name}',
+                'cyan'
+            )
+            ut.cprint(
+                f'Use width={width:.1f} in. or {width_cm:.1f} cm',
+                'cyan'
+            )
 
     if show:
         plt.show()
@@ -327,7 +375,7 @@ def plot_chit(chit: ArrayLike, temps: ArrayLike, fields: ArrayLike = None,
 
 def plot_ir(wavenumbers: ArrayLike, linear_absorbance: ArrayLike,
             lineshape: str = 'lorentzian', linewidth: float = 10.,
-            x_lim: list[float] = [None, None],
+            xlim: list[float] = [None, None],
             save: bool = False, save_name: str = 'ir.png', show: bool = False,
             window_title: str = 'Infrared spectrum'):
     '''
@@ -343,7 +391,7 @@ def plot_ir(wavenumbers: ArrayLike, linear_absorbance: ArrayLike,
         Lineshape function to use for each transition/signal
     linewidth: float
         Linewidth used in lineshape [cm^-1]
-    x_lim: list[float], default [None, None]
+    xlim: list[float], default [None, None]
         Minimum and maximum x-values to plot [cm^-1]
     save: bool, default False
         If True, plot is saved to save_name
@@ -362,8 +410,8 @@ def plot_ir(wavenumbers: ArrayLike, linear_absorbance: ArrayLike,
         'lorentzian': ut.lorentzian
     }
 
-    if None not in x_lim:
-        x_range = np.linspace(x_lim[0], x_lim[1], 100000)
+    if None not in xlim:
+        x_range = np.linspace(xlim[0], xlim[1], 100000)
     else:
         x_range = np.linspace(0, np.max(wavenumbers) * 1.1, 100000)
 
@@ -403,8 +451,8 @@ def plot_ir(wavenumbers: ArrayLike, linear_absorbance: ArrayLike,
 
 def plot_raman(wavenumbers: ArrayLike, intensities: ArrayLike,
                lineshape: str = 'gaussian', linewidth: float = 10.,
-               x_lim: list[float] = 0., x_unit: str = 'wavenumber',
-               abs_type: str = 'absorption', y_lim: list[float] = 'auto',
+               xlim: list[float] = 0., x_unit: str = 'wavenumber',
+               abs_type: str = 'absorption', ylim: list[float] = 'auto',
                save: bool = False, save_name: str = 'raman.png',
                show: bool = False,
                window_title: str = 'Raman spectrum'):
@@ -466,7 +514,9 @@ def plot_ailft_orb_energies(energies: ArrayLike, labels: ArrayLike = None,
         Matplotlib Axis object for plot
     '''
 
-    fig, ax = plt.subplots(1, 1, figsize=(3.5, 3.5), num=window_title)
+    width = 3.5
+    width_cm = width * 2.54
+    fig, ax = plt.subplots(1, 1, figsize=(width, width), num=window_title)
     ax.yaxis.set_minor_locator(AutoMinorLocator())
 
     if groups is not None:
@@ -497,27 +547,21 @@ def plot_ailft_orb_energies(energies: ArrayLike, labels: ArrayLike = None,
         if len(occupations) != len(energies):
             raise ValueError('Number of occupation numbers does not match number of states') # noqa
 
-        # Make spin up and spin down arrow markers
-        spup = mpl.markers.MarkerStyle(marker=r'$\leftharpoondown$')
-        spup._transform = spup.get_transform().rotate_deg(-90)
-
-        spdown = mpl.markers.MarkerStyle(marker=r'$\leftharpoondown$')
-        spdown._transform = spdown.get_transform().rotate_deg(90)
-
         # Plot each marker
+        _fd = {'size': 20, 'family': 'DejaVu Sans'}
+        va = 'center_baseline'
         for occ, en, xval in zip(occupations, energies, xvals):
-            lx = xval - 1 / 10
-            rx = xval + 1 / 10
+            lx = xval - 3 / 40
             # Up and down
             if occ == 2:
-                ax.scatter(lx, en, s=400, marker=spup, color='k', linewidths=0.001) # noqa
-                ax.scatter(rx, en, s=400, marker=spdown, color='k', lw=0.001)
+                ax.text(lx, en, s='↿', color='k', fontdict=_fd, va=va)
+                ax.text(lx + 1 / 40, en, s='⇂', color='k', fontdict=_fd, va=va)
             # up
             elif occ == 1:
-                ax.scatter(lx, en, s=400, marker=spup, color='k', lw=0.001)
+                ax.text(lx, en, s='↿', color='k', fontdict=_fd, va=va)
             # down
             elif occ == -1:
-                ax.scatter(rx, en, s=400, marker=spdown, color='k', lw=0.001)
+                ax.text(lx, en, s='⇂', color='k', fontdict=_fd, va=va)
 
     if labels is not None:
         for xval, energy, label in zip(xvals, energies, labels):
@@ -547,6 +591,7 @@ def plot_ailft_orb_energies(energies: ArrayLike, labels: ArrayLike = None,
         plt.savefig(save_name, dpi=500)
         if verbose:
             ut.cprint(f'\nAI-LFT orbitals saved to\n{save_name}', 'cyan')
+            ut.cprint(f'Use width={width:.1f} in. or {width_cm:.1f} cm', 'cyan') # noqa
 
     if show:
         plt.show()

orto/utils.py

@@ -2,6 +2,9 @@ import sys
 import os
 from numpy.typing import ArrayLike, NDArray
 import numpy as np
+from docx.oxml import OxmlElement
+from docx.oxml.ns import qn
+from docx.table import _Cell
 
 
 def red_exit(string):
@@ -411,9 +414,48 @@ def is_floatable(string: str) -> bool:
     bool
         True if string can be converted to float, False otherwise
     '''
-
     try:
         float(string)
         return True
     except ValueError:
         return False
+
+
+def set_cell_border(cell: _Cell, **kwargs):
+    """
+    Set cell`s border
+    Usage:
+
+    set_cell_border(
+        cell,
+        top={"sz": 12, "val": "single", "color": "#FF0000", "space": "0"},
+        bottom={"sz": 12, "color": "#00FF00", "val": "single"},
+        start={"sz": 24, "val": "dashed", "shadow": "true"},
+        end={"sz": 12, "val": "dashed"},
+    )
+    """
+    tc = cell._tc
+    tcPr = tc.get_or_add_tcPr()
+
+    # check for tag existence, if none found, then create one
+    tcBorders = tcPr.first_child_found_in("w:tcBorders")
+    if tcBorders is None:
+        tcBorders = OxmlElement('w:tcBorders')
+        tcPr.append(tcBorders)
+
+    # list over all available tags
+    for edge in ('start', 'top', 'end', 'bottom', 'insideH', 'insideV'):
+        edge_data = kwargs.get(edge)
+        if edge_data:
+            tag = 'w:{}'.format(edge)
+
+            # check for tag existence, if none found, then create one
+            element = tcBorders.find(qn(tag))
+            if element is None:
+                element = OxmlElement(tag)
+                tcBorders.append(element)
+
+            # looks like order of attributes is important
+            for key in ["sz", "val", "color", "space", "shadow"]:
+                if key in edge_data:
+                    element.set(qn('w:{}'.format(key)), str(edge_data[key]))

{orto-1.12.0.dist-info → orto-1.13.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.12.0
+Version: 1.13.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow
@@ -16,10 +16,10 @@ License-File: LICENSE
 Requires-Dist: numpy>=2.1.2
 Requires-Dist: xyz_py>=5.19.2
 Requires-Dist: matplotlib>=3.9.2
-Requires-Dist: extto>=1.0.1
+Requires-Dist: extto>=1.1.0
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: subto>=0.1.1
-Requires-Dist: python-docx>=1.1.2
+Requires-Dist: python-docx>=1.2.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

orto-1.13.1.dist-info/RECORD

@@ -0,0 +1,17 @@
+orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
+orto/__version__.py,sha256=AWOJJXuaKFwrwxYimWHjFlOhtOJuGrGuiJ0JN7ehebE,23
+orto/cli.py,sha256=gBc8sSq9L3FXoYEyYxFQRMCCGtTEaVaGjePXOAnLM8Y,106677
+orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
+orto/data.py,sha256=uHxgL-RIwQD61ZsrJPbrS0NBPDb3qIeLSbnpjlsPmiI,18225
+orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
+orto/extractor.py,sha256=nhrtzaeJtuU_SkMm201Z1ZqgHYnlsNfHxVOfVhs5plU,87484
+orto/input.py,sha256=uUQV6A-8D0GZpRoY1rKK_aUPmk9kVVTnMzTHuisP5t4,11888
+orto/job.py,sha256=tDiz9omFwinoYJamgz66MZez0Ee9HMhuCIAeHMhXRF8,5916
+orto/plotter.py,sha256=gw1oSPilWvUO__CjIq8gP9a8_Xq0078VE9porOPvhCc,19661
+orto/utils.py,sha256=2vMUQa_QPi7RbBdZN9EUara6A58GLZkJb9TfMTbBroU,11259
+orto-1.13.1.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+orto-1.13.1.dist-info/METADATA,sha256=k71QOiH_in85mH8YKiMRgSr2XTG_6O5ROqkHqxosiQ0,1185
+orto-1.13.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.13.1.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.13.1.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.13.1.dist-info/RECORD,,

orto-1.12.0.dist-info/RECORD

@@ -1,17 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=68GNJTQv5qIW_NND-ON34BeDlaBPM89Dp34LgcTS2k8,23
-orto/cli.py,sha256=s8w4_aQoT6PaEc8XR3kCb-nC0X9M_WAucKa693lc0BM,102887
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