orto 1.11.3__py3-none-any.whl → 1.13.0__py3-none-any.whl

orto/cli.py

@@ -79,16 +79,31 @@ def extract_sf_energies_func(uargs):
     from docx.enum.table import WD_ALIGN_VERTICAL
     from docx.shared import Pt
 
-    all_data = oe.SpinFreeEnergyExtractor().extract(
-        uargs.output_file
+    cas_energies = oe.SpinFreeEnergyExtractor().extract(
+        uargs.output_file,
+        before='NEVPT2 TRANSITION ENERGIES'
     )
 
+    # Extract NEVPT2 data
+    try:
+        nev_energies = oe.SpinFreeEnergyExtractor().extract(
+            uargs.output_file,
+            after='NEVPT2 TRANSITION ENERGIES'
+        )
+    except DataNotFoundError:
+        nev_energies = []
+    except (DataFormattingError, ValueError) as e:
+        ut.red_exit(str(e))
+
+    # Section names
+    names = ['CASSCF Results'] * len(cas_energies)
+    names += ['NEVPT2 Results'] * len(nev_energies)
+
     if uargs.output_format == 'txt':
         out_name = f'{uargs.output_file.stem}_sfenergies.txt'
         with open(out_name, 'w') as f:
-            for it, data in enumerate(all_data):
-                if len(all_data) > 1:
-                    f.write(f'# Section {it + 1:d}\n')
+            for it, data in enumerate(cas_energies + nev_energies):
+                f.write(f'{names[it]}\n')
 
                 f.write('State, Root, Multiplicity, Relative Energy (cm⁻¹)\n')
 
@@ -99,18 +114,23 @@ def extract_sf_energies_func(uargs):
                     f.write(
                         f'{rit + 1:d}, {data['root'][rit]:d}, {data['multiplicity'][rit]:d}, {data['delta energy (cm^-1)'][rit - 1]:.2f}\n' # noqa
                     )
-                if len(all_data) > 1:
+                if len(names) > 1:
                     f.write('-------------------\n')
 
     if uargs.output_format == 'docx':
         out_name = f'{uargs.output_file.stem}_sfenergies.docx'
 
-        title = 'Spin-Free energies'
-
         # Create document
         doc = Document()
 
-        doc.add_heading(title, 0)
+        # Add style
+        style = doc.styles['Normal']
+        font = style.font
+        font.name = 'Arial'
+        font.size = Pt(12)
+
+        title = 'Spin-Free energies'
+        doc.add_paragraph(title, style='Normal')
 
         # Add style
         style = doc.styles['Normal']
@@ -119,9 +139,8 @@ def extract_sf_energies_func(uargs):
         font.size = Pt(12)
 
         # For each extracted section, print matrix, vectors, and values
-        for it, data in enumerate(all_data):
-            if len(all_data) > 1:
-                doc.add_paragraph(f'\nSection {it + 1:d}\n')
+        for it, data in enumerate(cas_energies + nev_energies):
+            doc.add_paragraph(f'\n {names[it]}\n')
 
             # Table of data
             table = doc.add_table(rows=len(data['root']) + 1, cols=4)
@@ -134,6 +153,14 @@ def extract_sf_energies_func(uargs):
             ss.font.superscript = True
             table.cell(0, 3).paragraphs[0].add_run(')')
 
+            single = {"sz": 12, "color": "#000000", "val": "single"}
+            double = {"sz": 12, "color": "#000000", "val": "double"}
+
+            ut.set_cell_border(table.cell(0, 0), bottom=double, top=single)
+            ut.set_cell_border(table.cell(0, 1), bottom=double, top=single)
+            ut.set_cell_border(table.cell(0, 2), bottom=double, top=single)
+            ut.set_cell_border(table.cell(0, 3), bottom=double, top=single)
+
             # Add data
             for rit in range(len(data['root'])):
                 table.cell(rit + 1, 0).text = f'{rit + 1:d}'
@@ -144,6 +171,12 @@ def extract_sf_energies_func(uargs):
                 else:
                     table.cell(rit + 1, 3).text = f'{data['delta energy (cm^-1)'][rit - 1]:.2f}' # noqa
 
+            for cit in range(4):
+                ut.set_cell_border(
+                    table.cell(len(data['root']), cit),
+                    bottom=single
+                )
+
             for row in table.rows:
                 for cell in row.cells:
                     cell.paragraphs[0].paragraph_format.alignment = WD_ALIGN_PARAGRAPH.CENTER # noqa
@@ -169,15 +202,30 @@ def extract_so_energies_func(uargs):
     '''
     from . import extractor as oe
 
-    all_energies = oe.SpinOrbitEnergyExtractor().extract(
-        uargs.output_file
+    cas_energies = oe.SpinOrbitEnergyExtractor().extract(
+        uargs.output_file,
+        before='QDPT WITH NEVPT2 DIAGONAL ENERGIES'
     )
 
+    # Extract NEVPT2 data
+    try:
+        nev_energies = oe.SpinOrbitEnergyExtractor().extract(
+            uargs.output_file,
+            after='QDPT WITH NEVPT2 DIAGONAL ENERGIES'
+        )
+    except DataNotFoundError:
+        nev_energies = []
+    except (DataFormattingError, ValueError) as e:
+        ut.red_exit(str(e))
+
+    # Section names
+    names = ['CASSCF Results'] * len(cas_energies)
+    names += ['NEVPT2 Results'] * len(nev_energies)
+
     out_name = f'{uargs.output_file.stem}_soenergies.txt'
     with open(out_name, 'w') as f:
-        for it, energies in enumerate(all_energies):
-            if len(all_energies) > 1:
-                f.write(f'# Section {it + 1:d}\n')
+        for it, energies in enumerate(cas_energies + nev_energies):
+            f.write(f'{names[it]}\n')
 
             f.write('State, Relative Energy (cm⁻¹)\n')
 
@@ -185,7 +233,7 @@ def extract_so_energies_func(uargs):
                 f.write(
                     f'{eit + 1:d}, {energy:.4f}\n'
                 )
-            if len(all_energies) > 1:
+            if len(names) > 1:
                 f.write('-------------------\n')
 
     ut.cprint(f'Data written to {out_name}', 'cyan')
@@ -227,7 +275,7 @@ def extract_hyperfine_func(uargs, save=True):
         out_name = f'{uargs.output_file.stem}_hyperfine.txt'
         with open(out_name, 'w') as f:
             f.write(f'Data from {uargs.output_file}\n')
-            f.write('All values are in MHz')
+            f.write('All values are in MHz\n')
             for data in all_data:
                 if len(all_data) > 1:
                     f.write('=================\n')
@@ -402,7 +450,7 @@ def extract_gmatrix_func(uargs, save=True):
     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 docx.shared import Pt, RGBColor
 
     choices = {
         'total': oe.GMatrixExtractor,
@@ -416,63 +464,134 @@ def extract_gmatrix_func(uargs, save=True):
     if oe.EPRNMRDetector(uargs.output_file):
         uargs.type = 'dft'
 
-    try:
-        all_data = choices[uargs.type]().extract(uargs.output_file)
-    except (DataFormattingError, ValueError) as e:
-        ut.red_exit(str(e))
+    if uargs.type == 'dft':
+        cas_data, nev_data = [], []
+
+        # Extract DFT data
+        try:
+            dft_data = choices[uargs.type]().extract(
+                uargs.output_file
+            )
+        except DataNotFoundError:
+            dft_data = []
+        except (DataFormattingError, ValueError) as e:
+            ut.red_exit(str(e))
+    else:
+        dft_data = []
+
+        # Extract CASSCF data
+        try:
+            cas_data = choices[uargs.type]().extract(
+                uargs.output_file,
+                before='QDPT WITH NEVPT2 DIAGONAL ENERGIES',
+                after='QDPT WITH CASSCF DIAGONAL ENERGIES'
+            )
+        except (DataFormattingError, ValueError) as e:
+            ut.red_exit(str(e))
+
+        # Extract NEVPT2 data
+        try:
+            nev_data = choices[uargs.type]().extract(
+                uargs.output_file,
+                after='QDPT WITH NEVPT2 DIAGONAL ENERGIES'
+            )
+        except DataNotFoundError:
+            nev_data = []
+        except (DataFormattingError, ValueError) as e:
+            ut.red_exit(str(e))
 
     if not save:
-        for it, data in enumerate(all_data):
-            print(f'Section {it + 1:d}')
+        for it, data in enumerate(dft_data):
+            print('\nDFT Results')
             for key, val in data.items():
                 print(f'{key}:')
                 print(val)
+
+        for it, data in enumerate(cas_data):
+            print('\nCASSCF Results')
+            for key, val in data.items():
+                print(f'{key}:')
+                print(val)
+
+        for it, data in enumerate(nev_data):
+            print('\nNEVPT2 Results')
+            for key, val in data.items():
+                print(f'{key}:')
+                print(val)
+
         sys.exit(0)
 
+    titles = {
+        'total': 'ELECTRONIC G-MATRIX',
+        'L': 'ELECTRONIC G-MATRIX: L contribution',
+        'S': 'ELECTRONIC G-MATRIX: S contribution',
+        'eff': 'ELECTRONIC G-MATRIX FROM EFFECTIVE HAMILTONIAN',
+        'dft': 'ELECTRONIC G-MATRIX FROM DFT LINEAR RESPONSE'
+    }
+
     if uargs.output_format == 'txt':
         out_name = f'{uargs.output_file.stem}_gmatrix.txt'
         with open(out_name, 'w') as f:
-            for it, data in enumerate(all_data):
-                if len(all_data) > 1:
-                    f.write(f'Section {it + 1:d}\n')
-                for key, val in data.items():
-                    f.write(f'{key}:\n')
-                    f.write(str(val).replace('[', '').replace(']', ''))
-                    f.write('\n')
+            f.write(f'G Matrix data from {uargs.output_file}\n')
+            f.write(f'{titles[uargs.type]}\n')
+            f.write('=======================================\n')
+
+            if len(dft_data):
+                f.write('\nDFT Results\n')
+                for it, data in enumerate(dft_data):
+                    for key, val in data.items():
+                        f.write(f'{key}:\n')
+                        f.write(str(val).replace('[', '').replace(']', ''))
+                        f.write('\n')
+
+            if len(cas_data):
+                f.write('\nCASSCF Results\n')
+                for it, data in enumerate(cas_data):
+                    for key, val in data.items():
+                        f.write(f'{key}:\n')
+                        f.write(str(val).replace('[', '').replace(']', ''))
+                        f.write('\n')
+
+            if len(nev_data):
+                f.write('\nNEVPT2 Results\n')
+                for it, data in enumerate(nev_data):
+                    for key, val in data.items():
+                        f.write(f'{key}:\n')
+                        f.write(str(val).replace('[', '').replace(']', ''))
+                        f.write('\n')
 
     if uargs.output_format == 'docx':
         out_name = f'{uargs.output_file.stem}_gmatrix.docx'
 
-        titles = {
-            'total': 'ELECTRONIC G-MATRIX',
-            'L': 'ELECTRONIC G-MATRIX: L contribution',
-            'S': 'ELECTRONIC G-MATRIX: S contribution',
-            'eff': 'ELECTRONIC G-MATRIX FROM EFFECTIVE HAMILTONIAN',
-            'dft': 'ELECTRONIC G-MATRIX FROM DFT LINEAR RESPONSE'
-        }
-
-        title = titles[uargs.type]
-
         # Create document
         doc = Document()
 
-        doc.add_heading(title, 0)
-
         # Add style
         style = doc.styles['Normal']
         font = style.font
         font.name = 'Arial'
         font.size = Pt(12)
+        font.color.rgb = RGBColor(0, 0, 0)
+
+        title = titles[uargs.type]
+        doc.add_paragraph(title, style='Normal')
+        doc.add_paragraph(f'Data from {uargs.output_file}', style='Normal')
+
+        # Section names
+        names = ['CASSCF Results'] * len(cas_data)
+        names += ['NEVPT2 Results'] * len(nev_data)
+        names += ['DFT Results'] * len(dft_data)
 
         # For each extracted section, print matrix, vectors, and values
-        for it, data in enumerate(all_data):
-            if len(all_data) > 1:
-                doc.add_paragraph(f'Section {it + 1:d}')
+        for it, data in enumerate(cas_data + nev_data + dft_data):
+            doc.add_paragraph(f'{names[it]}', style='Normal')
 
             if uargs.type == 'eff':
                 doc.add_paragraph(f'Effective S={data['spin_mult']:2d}')
 
             # Full matrix
+            doc.add_paragraph('Full Matrix', style='Normal')
+
             matrix = doc.add_table(rows=3, cols=3)
 
             matrix.cell(0, 0).text = '{:.4f}'.format(data['matrix'][0, 0])
@@ -496,11 +615,17 @@ def extract_gmatrix_func(uargs, save=True):
                     cell.paragraphs[0].style = 'Normal'
 
             # g values and g vectors
+            doc.add_paragraph('Eigenpairs', style='Normal')
+
             table = doc.add_table(rows=4, cols=4)
             table.cell(0, 1).merge(table.cell(0, 1)).merge(table.cell(0, 2)).merge(table.cell(0, 3)) # noqa
 
+            single = {"sz": 12, "color": "#000000", "val": "single"}
+            double = {"sz": 12, "color": "#000000", "val": "double"}
             table.cell(0, 0).text = 'Values'
+            ut.set_cell_border(table.cell(0, 0), bottom=double, top=single)
             table.cell(0, 1).text = 'Vectors'
+            ut.set_cell_border(table.cell(0, 1), bottom=double, top=single)
 
             table.cell(1, 0).text = '{:.4f}'.format(data['values'][0])
             table.cell(2, 0).text = '{:.4f}'.format(data['values'][1])
@@ -518,12 +643,19 @@ def extract_gmatrix_func(uargs, save=True):
             table.cell(2, 3).text = '{:.4f}'.format(data['vectors'][2, 1])
             table.cell(3, 3).text = '{:.4f}'.format(data['vectors'][2, 2])
 
+            ut.set_cell_border(table.cell(3, 0), bottom=single)
+            ut.set_cell_border(table.cell(3, 1), bottom=single)
+            ut.set_cell_border(table.cell(3, 2), bottom=single)
+            ut.set_cell_border(table.cell(3, 3), bottom=single)
+
             for row in table.rows:
                 for cell in row.cells:
                     cell.paragraphs[0].paragraph_format.alignment = WD_ALIGN_PARAGRAPH.CENTER # noqa
                     cell.vertical_alignment = WD_ALIGN_VERTICAL.CENTER
                     cell.paragraphs[0].style = 'Normal'
 
+            if it != len(names) - 1:
+                doc.add_page_break()
         try:
             doc.save(out_name)
         except PermissionError:
@@ -537,9 +669,99 @@ def extract_gmatrix_func(uargs, save=True):
     return
 
 
+def gen_orbs_func(uargs):
+    '''
+    Wrapper for CLI gen orbs call
+
+    Parameters
+    ----------
+    uargs: argparser object
+        User arguments
+
+    Returns
+    -------
+    None
+    '''
+    from subto.job import SlurmJob
+
+    # Check orca module
+    if len(uargs.orca_load):
+        orca_load_val = copy.copy(uargs.orca_load)
+    elif os.getenv('orto_orca_load'):
+        try:
+            if len(os.getenv('orto_orca_load')):
+                orca_load_val = os.getenv('orto_orca_load')
+        except ValueError:
+            ut.red_exit(
+                (
+                    'Error in orto_orca_load environment variable'
+                )
+            )
+    else:
+        ut.red_exit(
+            (
+                'Missing orto_orca_load environment variable or '
+                '--orca_load argument'
+            )
+        )
+
+    # Create string of command numbers for orca plot to follow
+    command_nums = '1\\n1\\n4'
+    command_nums += f'\\n{uargs.n_pts:d}'
+    command_nums += '\\n5\\n7'
+
+    if uargs.beta:
+        command_nums += '\\n3\\n1'
+
+    for orbital_number in uargs.orb_numbers:
+        command_nums += '\\n2'
+        command_nums += f'\\n{orbital_number:d}'
+        command_nums += '\\n11'
+    command_nums += '\\n12\\n'
+
+    # Generate job file for orca_plot
+    orb_job = SlurmJob(
+        pathlib.Path(f'{uargs.gbw_file.stem}_orbital_job.sh')
+    )
+
+    # Create content of job
+    orb_job.content_block = ''
+
+    orb_job.content_block += '# Load orca module\n'
+    orb_job.content_block += f'module load {orca_load_val}\n'
+    orb_job.content_block += '# Run orca_plot to generate orbital cube file(s)\n' # noqa
+    orb_job.content_block += f'time mpirun -np {uargs.n_procs:d} $(which orca_plot_mpi) {uargs.gbw_file.name} -i aa <<< $\'{command_nums}\'\n\n' # noqa
+
+    # Set job name
+    orb_job.job_name = f'{uargs.gbw_file.stem}_orbitals'
+
+    orb_job.ntasks_per_node = str(uargs.n_procs)
+    orb_job.mem_per_cpu = str(uargs.memory)
+
+    orb_job.error = f'{uargs.gbw_file.stem}_orbitals.%j.e'
+    orb_job.output = f'{uargs.gbw_file.stem}_orbitals.%j.o'
+
+    # Write job script
+    # with submitter configuration options specified
+    orb_job.write_script(True)
+
+    # Submit to queue
+    if not uargs.no_sub:
+        subprocess.call(
+            'cd {}; {} "{}"; cd ../'.format(
+                uargs.gbw_file.parents[0],
+                orb_job.SUBMIT_COMMAND,
+                orb_job.file_path
+                ),
+            shell=True
+        )
+
+    return
+
+
 def gen_spden_func(uargs):
     '''
-    Wrapper for CLI gen spin density call
+    Wrapper for CLI gen spin_density call
 
     Parameters
     ----------
@@ -868,7 +1090,6 @@ def plot_xes_func(uargs):
     None
     '''
     import matplotlib.pyplot as plt
-    import matplotlib as mpl
     from . import plotter
     from . import extractor as oe
 
@@ -876,7 +1097,8 @@ def plot_xes_func(uargs):
     ut.check_font_envvar()
 
     # Change matplotlib font size to be larger
-    mpl.rcParams.update({'font.size': 12})
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
 
     version = oe.OrcaVersionExtractor.extract(uargs.output_file)
 
@@ -956,8 +1178,8 @@ def plot_xes_func(uargs):
             show=_SHOW_CONV[uargs.plot],
             save=_SAVE_CONV[uargs.plot],
             save_name=save_name,
-            x_lim=uargs.x_lim,
-            y_lim=uargs.y_lim,
+            xlim=uargs.xlim,
+            ylim=uargs.ylim,
             x_shift=uargs.shift,
             linewidth=uargs.linewidth,
             lineshape=uargs.lineshape,
@@ -972,112 +1194,6 @@ def plot_xes_func(uargs):
         plt.show()
 
 
-def plot_xas_func(uargs):
-    '''
-    Wrapper for CLI plot xas call
-
-    Parameters
-    ----------
-    uargs: argparser object
-        User arguments
-
-    Returns
-    -------
-    None
-    '''
-    import matplotlib.pyplot as plt
-    import matplotlib as mpl
-    from . import plotter
-    from . import extractor as oe
-
-    # Set user specified font name
-    ut.check_font_envvar()
-
-    # Change matplotlib font size to be larger
-    mpl.rcParams.update({'font.size': 12})
-
-    version = oe.OrcaVersionExtractor.extract(uargs.output_file)
-
-    if not len(version):
-        ut.cprint(
-            'Warning: Cannot find version number in Orca output file',
-            'black_yellowbg'
-        )
-        version = [6, 0, 0]
-
-    if version[0] >= 6:
-        if uargs.intensities == 'electric':
-            all_data = oe.XASElectricDipoleExtractor.extract(
-                uargs.output_file
-            )
-        elif uargs.intensities == 'velocity':
-            all_data = oe.XASVelocityDipoleExtractor.extract(
-                uargs.output_file
-            )
-        elif uargs.intensities == 'semi-classical':
-            all_data = oe.XASSemiClassicalDipoleExtractor.extract(
-                uargs.output_file
-            )
-    elif version[0] < 6:
-        ut.red_exit('Unsupported version of Orca for XAS extraction', 'red')
-
-    ut.cprint('Using intensities: {}'.format(uargs.intensities), 'cyan')
-
-    # Plot each section
-    for it, data in enumerate(all_data):
-
-        if len(all_data) > 1:
-            save_name = f'absorption_spectrum_section_{it:d}.png'
-        else:
-            save_name = 'absorption_spectrum.png'
-
-        if uargs.x_unit == 'wavenumber':
-            x_values = np.asarray(data['energy (cm^-1)'])
-        elif uargs.x_unit == 'wavelength':
-            x_values = 1E7 / np.asarray(data['energy (cm^-1)'])
-        elif uargs.x_unit == 'energy':
-            x_values = np.asarray(data['energy (ev)'])
-
-        data['fosc'] = np.asarray(data['fosc'])
-
-        # Remove transitions with zero oscillator strength from
-        # beginning and end of spectrum
-        print(data['fosc'], x_values)
-        if not uargs.no_trim:
-            # Find first non-zero oscillator strength
-            first_nonzero = np.where(data['fosc'] > 1E-6)[0][0]
-            # Find last non-zero oscillator strength
-            last_nonzero = np.where(data['fosc'] > 1E-6)[0][-1]
-
-            # Trim data
-            x_values = x_values[first_nonzero:last_nonzero + 1]
-            data['fosc'] = data['fosc'][first_nonzero:last_nonzero + 1]
-
-        # Plot absorption spectrum
-        fig, ax = plotter.plot_abs(
-            x_values,
-            uargs.x_unit,
-            data['fosc'],
-            show=_SHOW_CONV[uargs.plot],
-            save=_SAVE_CONV[uargs.plot],
-            save_name=save_name,
-            x_lim=uargs.x_lim,
-            y_lim=uargs.y_lim,
-            x_shift=uargs.shift,
-            linewidth=uargs.linewidth,
-            lineshape=uargs.lineshape,
-            window_title=f'Absorption Spectrum from {uargs.output_file}',
-            osc_style=uargs.osc_style,
-            normalise=uargs.normalise
-        )
-
-        if uargs.x_unit == 'wavenumber':
-            ax[0].set_xlim([0, 50000])
-        plt.show()
-
-    return
-
-
 def plot_abs_func(uargs, save_data_only=False):
     '''
     Wrapper for CLI plot abs call\n\n
@@ -1102,7 +1218,6 @@ def plot_abs_func(uargs, save_data_only=False):
     from . import extractor as oe
     from . import data as d
 
-
     # Process x_shift argument
     if uargs.x_shift is None:
         uargs.x_shift = [0.0 for _ in uargs.output_file]
@@ -1174,9 +1289,9 @@ def plot_abs_func(uargs, save_data_only=False):
         # report if multiple absorption sections found
         elif len(all_abs_data) > 1:
             ut.cprint(
-                f'Found {len(all_abs_data)} ABSORPTION sections in '
+                f'\nFound {len(all_abs_data)} ABSORPTION sections in '
                 f'file {output_file}\n'
-                f'Plotting final section ONLY',
+                f'Plotting final section ONLY\n',
                 'cyan'
             )
         # and only use final one
@@ -1208,25 +1323,25 @@ def plot_abs_func(uargs, save_data_only=False):
 
         # Set x_min
         # based on user arguments
-        if isinstance(uargs.x_lim[0], str):
-            if uargs.x_lim[0] == 'auto':
+        if isinstance(uargs.xlim[0], str):
+            if uargs.xlim[0] == 'auto':
                 x_min = min(x_vals) * min_factor
-            elif ut.is_floatable(uargs.x_lim[0]):
-                x_min = float(uargs.x_lim[0])
+            elif ut.is_floatable(uargs.xlim[0]):
+                x_min = float(uargs.xlim[0])
             else:
-                raise ValueError(f'Invalid x_min value: {uargs.x_lim[0]}')
+                raise ValueError(f'Invalid x_min value: {uargs.xlim[0]}')
         else:
-            x_min = uargs.x_lim[0]
+            x_min = uargs.xlim[0]
 
         # Set x_max
         # based on user arguments
-        if isinstance(uargs.x_lim[1], str):
-            if uargs.x_lim[1] == 'auto':
+        if isinstance(uargs.xlim[1], str):
+            if uargs.xlim[1] == 'auto':
                 x_max = max(x_vals) * max_factor
-            elif ut.is_floatable(uargs.x_lim[1]):
-                x_max = float(uargs.x_lim[1])
+            elif ut.is_floatable(uargs.xlim[1]):
+                x_max = float(uargs.xlim[1])
             else:
-                raise ValueError(f'Invalid x_max value: {uargs.x_lim[1]}')
+                raise ValueError(f'Invalid x_max value: {uargs.xlim[1]}')
         else:
             x_max = uargs.xlim[1]
 
@@ -1265,27 +1380,27 @@ def plot_abs_func(uargs, save_data_only=False):
                 )
             )
             ut.cprint(
-                f'Saved absorption data to absorption_spectrum_{output_file.stem}.csv', # noqa
+                f'Saved absorption spectrum to absorption_spectrum_{output_file.stem}.csv', # noqa
                 'cyan'
             )
             ut.cprint(
-                f'Saved absorption spectrum data to transition_data_{output_file.stem}.csv', # noqa
+                f'Saved absorption data to transition_data_{output_file.stem}.csv', # noqa
                 'cyan'
             )
         else:
-            # Add to dictionary of spectra for plotting later
+            # Add to dictionary of absorption data for plotting later
             spectra_dict[output_file] = abs_data
 
     # Exit if only saving data
     if save_data_only:
         return
 
-    ## Plot all spectra
+    # Plot all spectra
     import matplotlib.pyplot as plt
     import matplotlib.colors as mcolors
 
     # Set font name and size
-    plt.rcParams['font.family'] = 'Arial'
+    ut.check_font_envvar()
     plt.rcParams['font.size'] = 10
     plt.rcParams['legend.fontsize'] = 9
     plt.rcParams['legend.loc'] = 'center right'
@@ -1302,7 +1417,7 @@ def plot_abs_func(uargs, save_data_only=False):
     if len(spectra_dict) > 1:
         width = 6.
     else:
-        width = 4
+        width = 3.425
     # width in cm
     width_cm = 2.54 * width
 
@@ -1324,7 +1439,7 @@ def plot_abs_func(uargs, save_data_only=False):
         plotter.plot_absorption_spectrum(
             abs_data,
             linecolor=colours[it],
-            stickcolour=colours[it],
+            stickcolor=colours[it],
             osc_style=uargs.osc_style,
             normalise=uargs.normalise,
             window_title='',
@@ -1333,14 +1448,14 @@ def plot_abs_func(uargs, save_data_only=False):
             oax=oax,
             show=False,
             save=False,
-            x_lim=[x_min, x_max],
-            y_lim=uargs.y_lim,
+            xlim=[x_min, x_max],
+            ylim=uargs.ylim,
             x_shift=uargs.x_shift[it],
             legend=False
         )
 
-    if uargs.x_lim != ['auto', 'auto']:
-        ax.set_xlim(float(uargs.x_lim[0]), float(uargs.x_lim[1]))
+    if uargs.xlim != ['auto', 'auto']:
+        ax.set_xlim(float(uargs.xlim[0]), float(uargs.xlim[1]))
 
     fig.tight_layout()
 
@@ -1355,7 +1470,7 @@ def plot_abs_func(uargs, save_data_only=False):
             fig.legend(uargs.legend, loc=7)
 
     if _SAVE_CONV[uargs.plot]:
-        savename = f'absorption_spectrum_{output_file.stem}.png'
+        savename = 'absorption_spectrum.png'
         plt.savefig(savename, dpi=500)
         ut.cprint(f'Saved image to {savename}', 'cyan')
         ut.cprint(
@@ -1382,7 +1497,7 @@ def plot_ir_func(uargs):
     -------
     None
     '''
-    import matplotlib as mpl
+    import matplotlib.pyplot as plt
     from . import plotter
     from . import extractor as oe
 
@@ -1390,7 +1505,8 @@ def plot_ir_func(uargs):
     ut.check_font_envvar()
 
     # Change matplotlib font size to be larger
-    mpl.rcParams.update({'font.size': 12})
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
 
     # Extract frequency information
     data = oe.FrequencyExtractor.extract(uargs.output_file)
@@ -1776,37 +1892,107 @@ def plot_susc_func(uargs) -> None:
         None
 
     '''
-    import matplotlib.pyplot as plt
-    import matplotlib as mpl
-    from . import plotter
     from . import extractor as oe
+    from . import data as d
 
-    # Change matplotlib font size to be larger
-    mpl.rcParams.update({'font.size': 12})
+    # Extract data from file before NEV section
+    try:
+        data = oe.SusceptibilityExtractor.extract(
+            uargs.output_file,
+            before='QDPT WITH NEVPT2 DIAGONAL ENERGIES'
+        )
+    except DataNotFoundError:
+        data = []
 
-    # Extract data from file
-    data = oe.SusceptibilityExtractor.extract(uargs.output_file)
+    try:
+        data_nev = oe.SusceptibilityExtractor.extract(
+            uargs.output_file,
+            after='QDPT WITH NEVPT2 DIAGONAL ENERGIES'
+        )
+    except DataNotFoundError:
+        data_nev = []
 
-    if not len(data):
+    if not len(data + data_nev):
         ut.red_exit(
-            f'Cannot find susceptibility output in {uargs.output_file}'
+            f'Cannot find susceptibility data in {uargs.output_file}'
         )
 
-    if not uargs.quiet:
-        ut.cprint(
-            f'Found {len(data)} susceptibility blocks in file...',
-            'green'
+    # Create susceptibilitydata objects, one per data section
+    susc_data = d.SusceptibilityData.from_extractor_data(data)
+    nev_susc_data = d.SusceptibilityData.from_extractor_data(data_nev)
+
+    if uargs.nev_only:
+        susc_data = []
+
+    # Plot all data
+    import matplotlib.pyplot as plt
+    import matplotlib.colors as mcolors
+    from . import plotter
+
+    # Set font name and size
+    ut.check_font_envvar()
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
+
+    # Create list of colours for plotting
+    if len(susc_data + nev_susc_data) == 1:
+        colours = ['black']
+    else:
+        colours = list(mcolors.TABLEAU_COLORS.values())
+
+    # Width of figure in inches
+    # Make wider if multiple spectra to plot
+    # to include legend
+    if len(susc_data + nev_susc_data) > 1 and uargs.legend_separate:
+        width = 6.
+    else:
+        width = 3.425
+    # width in cm
+    width_cm = 2.54 * width
+
+    # Create figure and axis with
+    # height based on golden ratio for 4 inch wide figure
+    golden = (1 + np.sqrt(5))/2
+    height = 4. / golden
+    fig, ax = plt.subplots(
+        1,
+        1,
+        num='Magnetic Susceptibility',
+        figsize=(width, height)
+    )
+
+    for it, sd in enumerate(susc_data):
+        plotter.plot_susceptibility(
+            sd,
+            uargs.y_style,
+            linecolor=colours[it],
+            xlim=uargs.xlim,
+            ylim=uargs.ylim,
+            save=False,
+            show=False,
+            fig=fig,
+            ax=ax
         )
-        ut.cprint(
-            '... plotting each separately',
-            'green'
+
+    for it, sd in enumerate(nev_susc_data):
+        plotter.plot_susceptibility(
+            sd,
+            uargs.y_style,
+            linecolor=colours[it + len(susc_data)],
+            label=f'Calculated NEVPT2 ($H$ = {sd.field:.1f} Oe)',
+            save=False,
+            show=False,
+            fig=fig,
+            ax=ax
         )
 
     if uargs.exp_file is not None:
+
         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('#')
+                [row for row in csvfile if not row.startswith('#')],
+                skipinitialspace=True
             )
             for row in reader:
                 exp_data['Temperature (K)'].append(
@@ -1816,60 +2002,54 @@ def plot_susc_func(uargs) -> None:
                     float(row['chi*T (cm3*K/mol)'])
                 )
 
-    # Conversion factors from cm3 K mol^-1 to ...
-    convs = {
-        'A3 K': 1E24 / cst.AVOGADRO,
-        'A3 mol-1 K': 1E24,
-        'cm3 K': 1 / cst.AVOGADRO,
-        'cm3 mol-1 K': 1,
-        'emu K': 1 / (4 * np.pi * cst.AVOGADRO),
-        'emu mol-1 K': 1 / (4 * np.pi)
-    }
+        # Conversion factors to cm3 K mol^-1 from ...
+        convs = {
+            'A3 K': 1E24 / cst.AVOGADRO,
+            'A3 mol-1 K': 1E24,
+            'cm3 K': 1 / cst.AVOGADRO,
+            'cm3 mol-1 K': 1,
+            'emu K': 1 / (4 * np.pi * cst.AVOGADRO),
+            'emu mol-1 K': 1 / (4 * np.pi)
+        }
 
-    unit_labels = {
-        'A3 K': r'\AA^3\,K',
-        'A3 mol-1 K': r'\AA^3\,mol^{-1}\,K',
-        'cm3 K': r'cm^3\,K',
-        'cm3 mol-1 K': r'cm^3\,mol^{-1}\,K',
-        'emu K': r'emu\,K',
-        'emu mol-1 K': r'emu\,mol^{-1} \ K',
-    }
+        ax.plot(
+            exp_data['Temperature (K)'],
+            [
+                val * convs[uargs.esusc_units]
+                for val in exp_data['chi*T (cm3*K/mol)']
+            ],
+            lw=0,
+            marker='o',
+            fillstyle='none',
+            mew=.3,
+            color='k',
+            label='Experiment'
+        )
 
-    for dataframe in data:
-
-        fig, ax = plotter.plot_chit(
-            dataframe['chi*T (cm3*K/mol)'] * convs[uargs.susc_units],
-            dataframe['Temperature (K)'],
-            fields=dataframe['Static Field (Gauss)'],
-            window_title=f'Susceptibility from {uargs.output_file}',
-            y_unit=unit_labels[uargs.susc_units],
-            show=_SHOW_CONV[uargs.plot] if uargs.exp_file is None else False,
-            save=_SAVE_CONV[uargs.plot] if uargs.exp_file is None else False,
-        )
-        if uargs.exp_file is not None:
-            ax.plot(
-                exp_data['Temperature (K)'],
-                [
-                    val * convs[uargs.esusc_units]
-                    for val in exp_data['chi*T (cm3*K/mol)']
-                ],
-                lw=0,
-                marker='o',
-                fillstyle='none',
-                color='k',
-                label='Experiment'
-            )
-            fig.tight_layout()
-            ax.legend(frameon=False)
+    # Set x and y limits
+    plotter.set_axlims(ax, 'x', uargs.xlim)
+    plotter.set_axlims(ax, 'y', uargs.ylim)
+
+    fig.tight_layout()
 
-            _ylim = ax.get_ylim()
-            ax.set_ylim(0, _ylim[1])
+    if len(susc_data + nev_susc_data) > 1 or uargs.exp_file is not None:
+        if uargs.legend_separate:
+            fig.subplots_adjust(right=3.3/6.)
+            fig.legend(loc='center right')
+        else:
+            ax.legend(loc='best')
 
-            if _SAVE_CONV[uargs.plot]:
-                plt.savefig('chit_vs_t.png', dpi=500)
+    if _SAVE_CONV[uargs.plot]:
+        savename = 'susceptibility.png'
+        plt.savefig(savename, dpi=500)
+        ut.cprint(f'Saved image to {savename}', 'cyan')
+        ut.cprint(
+            f'Use width={width:.1f} in. or {width_cm:.1f} cm',
+            'cyan'
+        )
 
-            if _SHOW_CONV[uargs.plot]:
-                plt.show()
+    if _SHOW_CONV[uargs.plot]:
+        plt.show()
 
     return
 
@@ -1888,12 +2068,14 @@ def plot_ailft_func(uargs) -> None:
         None
     '''
     import matplotlib.pyplot as plt
-    import matplotlib as mpl
     from . import plotter
     from . import extractor as oe
 
+    # Set user specified font name
+    ut.check_font_envvar()
     # Change matplotlib font size to be larger
-    mpl.rcParams.update({'font.size': 12})
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
 
     # Create extractor
     data = oe.AILFTOrbEnergyExtractor.extract(uargs.output_file)
@@ -2081,6 +2263,7 @@ def read_args(arg_list=None):
 
     extract_hyperfine.add_argument(
         '--output_format',
+        '-of',
         type=str,
         help='Format of outputted data file',
         choices=['txt', 'docx'],
@@ -2112,6 +2295,7 @@ def read_args(arg_list=None):
 
     extract_gmatrix.add_argument(
         '--output_format',
+        '-of',
         type=str,
         help='Format of outputted data file',
         choices=['txt', 'docx'],
@@ -2135,6 +2319,7 @@ def read_args(arg_list=None):
 
     extract_sfenergies.add_argument(
         '--output_format',
+        '-of',
         type=str,
         help='Format of outputted data file',
         choices=['txt', 'docx'],
@@ -2203,6 +2388,89 @@ def read_args(arg_list=None):
         )
     )
 
+    gen_orbs = gen_parser.add_parser(
+        'orbs',
+        aliases=['orbitals', 'mos', 'mo'],
+        description='Generate molecular orbital cube file(s) from gbw file', # noqa
+        usage=ut.cstring(
+            'orto gen orbs <gbw_file> <orbs> <n_procs> [options]',
+            'cyan'
+        ),
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+    gen_orbs._positionals.title = 'Mandatory Arguments'
+    gen_orbs.set_defaults(func=gen_orbs_func)
+
+    gen_orbs.add_argument(
+        'gbw_file',
+        type=pathlib.Path,
+        help='Orca gbw file name'
+    )
+
+    gen_orbs.add_argument(
+        'orb_numbers',
+        type=int,
+        nargs='+',
+        help=(
+            'Orbital number(s) to generate cube file for'
+            '(these are alpha spin by default)'
+        )
+    )
+
+    gen_orbs.add_argument(
+        'n_procs',
+        type=int,
+        help='Number of processors/cores used in calculation',
+        default=1
+    )
+
+    gen_orbs.add_argument(
+        '--n_pts',
+        '-n',
+        type=int,
+        default=100,
+        help=(
+            'Number of points in each dimension of cube file\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_orbs.add_argument(
+        '--memory',
+        '-mem',
+        type=int,
+        default=500,
+        help=(
+            'Per-core Memory to use in MB\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_orbs.add_argument(
+        '-om',
+        '--orca_load',
+        type=str,
+        default='',
+        help='Orca environment module (overrides ORTO_ORCA_LOAD envvar)'
+    )
+
+    gen_orbs.add_argument(
+        '--beta',
+        action='store_true',
+        help=(
+            'Plot beta orbitals instead of alpha (for open shell calculations)'
+        )
+    )
+
+    gen_orbs.add_argument(
+        '--no_sub',
+        '-ns',
+        action='store_true',
+        help=(
+            'Disables submission of job to queue'
+        )
+    )
+
     gen_spden = gen_parser.add_parser(
         'spdens',
         aliases=['spin_density', 'spden'],
@@ -2435,6 +2703,7 @@ def read_args(arg_list=None):
 
     gen_abs.add_argument(
         '--x_unit',
+        '-xu',
         type=str,
         choices=['energy', 'wavelength', 'wavenumber'],
         default='energy',
@@ -2463,7 +2732,7 @@ def read_args(arg_list=None):
     )
 
     gen_abs.add_argument(
-        '--x_lim',
+        '--xlim',
         nargs=2,
         default=['auto', 'auto'],
         help='x limits of spectrum'
@@ -2603,6 +2872,7 @@ def read_args(arg_list=None):
 
     plot_abs.add_argument(
         '--x_unit',
+        '-xu',
         type=str,
         choices=['energy', 'wavelength', 'wavelength_rev', 'wavenumber'],
         default='energy',
@@ -2621,14 +2891,14 @@ def read_args(arg_list=None):
     )
 
     plot_abs.add_argument(
-        '--x_lim',
+        '--xlim',
         nargs=2,
         default=['auto', 'auto'],
         help='x limits of spectrum'
     )
 
     plot_abs.add_argument(
-        '--y_lim',
+        '--ylim',
         nargs=2,
         default=[0., 'auto'],
         help='Epsilon limits of spectrum in cm^-1 mol^-1 L'
@@ -2799,14 +3069,14 @@ def read_args(arg_list=None):
     )
 
     plot_xes.add_argument(
-        '--x_lim',
+        '--xlim',
         nargs=2,
         default=['auto', 'auto'],
         help='x limits of spectrum'
     )
 
     plot_xes.add_argument(
-        '--y_lim',
+        '--ylim',
         nargs=2,
         default=[0., 'auto'],
         help='Epsilon limits of spectrum in cm^-1 mol^-1 L'
@@ -2918,6 +3188,29 @@ def read_args(arg_list=None):
         help='Orca output file name'
     )
 
+    plot_susc.add_argument(
+        '--y_style',
+        '-ys',
+        type=str,
+        metavar='<str>',
+        choices=['X', 'XT', '1/X'],
+        default='XT'
+    )
+
+    plot_susc.add_argument(
+        '--xlim',
+        nargs=2,
+        default=['auto', 'auto'],
+        help='x limits of plot'
+    )
+
+    plot_susc.add_argument(
+        '--ylim',
+        nargs=2,
+        default=[0., 'auto'],
+        help='y limits of plot'
+    )
+
     plot_susc.add_argument(
         '--susc_units',
         '-su',
@@ -2987,6 +3280,20 @@ def read_args(arg_list=None):
         )
     )
 
+    plot_susc.add_argument(
+        '--nev_only',
+        '-no',
+        action='store_true',
+        help='Only plot NEVPT2 data'
+    )
+
+    plot_susc.add_argument(
+        '--legend_separate',
+        '-ls',
+        action='store_true',
+        help='Plot legend next to plot'
+    )
+
     plot_susc.add_argument(
         '--quiet',
         action='store_true',