Isopydistort

https://frandsengroup.github.io/isopydistort/
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Isopydistort provides tools for interfacing with the ISODISTORT web server, enabling users to...
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### get(cifname, outfname, method=3, var_dict={}, isoformat='topas', selection=1, subcif='', specify=False, basis=[])

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Interacts with the ISODISTORT website to get distortion modes and save the output to a file.

```APIDOC
## get(cifname, outfname, method=3, var_dict={}, isoformat='topas', selection=1, subcif='', specify=False, basis=[])

### Description
Interacts with the ISODISTORT website to get distortion modes. This function uploads a CIF file, processes it using the specified ISODISTORT method, and saves the resulting data to the provided output filename.

### Parameters
- **cifname** (str) - Required - The name of the local cif file you want to use.
- **outfname** (str) - Required - The name of the file where you want the ISODISTORT output saved.
- **method** (int) - Optional - Method number to be used by the ISODISTORT server (currently 3 or 4). Default is 3.
- **var_dict** (dict) - Optional - Variables to pass to ISODISTORT to set up the subgroup symmetry, lattice, and basis.
- **isoformat** (str) - Optional - Format of the output file requested from the ISODISTORT server. Allowed values: 'isovizdistortion', 'isovizdiffraction', 'structurefile', 'distortionfile', 'domains', 'primary', 'modesdetails', 'completemodesdetails', 'topas', 'fullprof', 'irreps', 'tree'. Default is 'topas'.
- **selection** (int) - Optional - The number of the desired distortion from the list of possible distortions provided by ISODISTORT, starting from 1. Default is 1.
- **subcif** (str) - Optional - Sub-CIF file path.
- **specify** (bool) - Optional - Flag to specify settings.
- **basis** (list) - Optional - Basis configuration list.
```

--------------------------------

### get(cifname, outfname, method=3, var_dict={}, isoformat='topas', selection=1, subcif='', specify=False, basis=[])

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Interacts with the ISODISTORT website to retrieve distortion modes based on a provided CIF file and configuration parameters.

```APIDOC
## get(cifname, outfname, method=3, var_dict={}, isoformat='topas', selection=1, subcif='', specify=False, basis=[])

### Description
Interacts with the ISODISTORT website to get distortion modes. This function handles the communication with the ISODISTORT server to process structural data.

### Parameters
- **cifname** (str) - Required - The name of the local cif file you want to use.
- **outfname** (str) - Required - The name of the file where you want the ISODISTORT output saved.
- **method** (int) - Optional - Method number to be used by the ISODISTORT server (currently 3 or 4).
- **var_dict** (dict) - Optional - Variables to pass to ISODISTORT to set up the subgroup symmetry, lattice, and basis.
- **isoformat** (str) - Optional - The format of the output.
- **selection** (int) - Optional - Selection parameter for the server.
- **subcif** (str) - Optional - Subcif configuration string.
- **specify** (bool) - Optional - Whether to specify a custom basis.
- **basis** (list) - Optional - List of 9 elements defining the basis if specify is True.
```

--------------------------------

### get(cifname, outfname, method=3, var_dict={}, isoformat='topas', selection=1, subcif='', specify=False, basis=[])

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Interacts with the ISODISTORT website to process CIF files and retrieve distortion modes based on the specified method and format.

```APIDOC
## get(cifname, outfname, method=3, var_dict={}, isoformat='topas', selection=1, subcif='', specify=False, basis=[])

### Description
Interacts with the ISODISTORT website to get distortion modes. This function handles the upload of a parent CIF file, applies the requested distortion method, and saves the output to a specified file.

### Parameters
- **cifname** (str) - Required - The name of the local CIF file to use.
- **outfname** (str) - Required - The name of the file where the ISODISTORT output will be saved.
- **method** (int) - Optional - Method number to be used by the ISODISTORT server (currently 3 or 4). Default is 3.
- **var_dict** (dict) - Optional - Variables to pass to ISODISTORT to set up subgroup symmetry, lattice, and basis.
- **isoformat** (str) - Optional - Format of the output file requested. Allowed values: 'isovizdistortion', 'isovizdiffraction', 'structurefile', 'distortionfile', 'domains', 'primary', 'modesdetails', 'completemodesdetails', 'topas', 'fullprof', 'irreps', 'tree'. Default is 'topas'.
- **selection** (int) - Optional - The number of the desired distortion from the list provided by ISODISTORT. Default is 1.
- **subcif** (str) - Optional - Sub-CIF file identifier for method 4.
- **specify** (bool) - Optional - Flag for method 4 configuration.
- **basis** (list) - Optional - Basis configuration for method 4.
```

--------------------------------

### Initialize isopydistort package

Source: https://frandsengroup.github.io/isopydistort/index.html

The package entry point imports the isoget module to enable web server interfacing.

```python
#!/usr/bin/env python
##############################################################################
#
# isopydistort        by Frandsen Group
#                     Benjamin A. Frandsen benfrandsen@byu.edu
#                     (c) 2023 Benjamin Allen Frandsen
#                      All rights reserved
#
# File coded by:    Benjamin Frandsen
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
#
##############################################################################

"""Tools for interfacing with the ISODISTORT web server.
"""

import isopydistort.isoget

# End of file
```

--------------------------------

### Execute test suite

Source: https://frandsengroup.github.io/isopydistort/tests/tests.html

Standard entry point for running the unittest suite.

```python
if __name__ == '__main__':
    unittest.main()
```

--------------------------------

### Configure ISODISTORT basis and parameters

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Sets up the basis variables and default parameters for the ISODISTORT request.

```python
    if specify == True:
        basis_vars = ["basis11", "basis12", "basis13", "basis21", "basis22", "basis23", "basis31", "basis32", "basis33"]
        if not basis:
            print("No basis specified. Exiting...")
            print("Try specifying a basis or setting specify to False")
        if len(basis) != 9:
            print("Incorrect number of elements for basis, expected 9")
        else:
            data['inputbasis'] = 'specify'
            for i in range(len(basis_vars)):
                data[basis_vars[i]] = f'{basis[i]}'

    data['chooseorigin'] = False
    data['trynearest'] = True
    data['dmax'] = 1
    data['zeromodes'] = False

    for key, value in var_dict.items():
        data[key] = value

    return data
```

--------------------------------

### Initialize ISODISTORT interaction

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Main entry point for interacting with the ISODISTORT website to retrieve distortion modes.

```python
def get(cifname, outfname, method=3, var_dict={}, isoformat='topas', selection=1, subcif = "", specify = False, basis = []):
    """Interacts with the ISODISTORT website to get distortion modes.

    Args:
        cifname (str): The name of the local cif file you want to use.
        outfname (str): The name of the file where you want the ISODISTORT
            output saved.
        method (int): Method number to be used by the ISODISTORT server. The
            currently available method numbers are 3 and 4.
        var_dict (dict): Variables to pass to ISODISTORT to set up the
            subgroup symmetry, lattice, and basis. The required dictionary
            keys depend on the method number chosen, as described below.
```

--------------------------------

### Method 3 Configuration Keys

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Required dictionary keys for Method 3 configuration.

```python
'subgroupsym' = '1 P1 C1-1'

'pointgroupsym' = '0'

'latticetype' = 'direct'

'centering' = 'd' (for default)

'basis11' = '1'

'basis12' = '0'

'basis13' = '0'

'basis21' = '0'

'basis22' = '1'
```

--------------------------------

### Method 3 Configuration Defaults

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Default dictionary keys and values for Method 3, which defaults to P1 symmetry and an identity matrix for the supercell basis.

```python
'subgroupsym' = '1 P1 C1-1'
'pointgroupsym' = '0'
'latticetype' = 'direct'
'centering' = 'd' (for default)
'basis11' = '1'
'basis12' = '0'
'basis13' = '0'
'basis21' = '0'
'basis22' = '1'
'basis23' = '0'
'basis31' = '0'
'basis32' = '0'
'basis33' = '1'
```

--------------------------------

### Execute unit tests for isopydistort

Source: https://frandsengroup.github.io/isopydistort/tests/tests.html

Run the unit tests using the Python interpreter.

```bash
python -m isopydistort.tests.tests
```

--------------------------------

### Configure ISODISTORT Basis Parameters

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Set the basis configuration values for the ISODISTORT server request.

```text
'basis23' = '0'

'basis31' = '0'

'basis32' = '0'

'basis33' = '1'
```

--------------------------------

### Build test suite

Source: https://frandsengroup.github.io/isopydistort/tests/index.html

Constructs a unittest.TestSuite object by dynamically importing modules defined in the modulenames list.

```python
def testsuite():
    '''Build a unit tests suite for the isopydistort package.
    Return a unittest.TestSuite object.
    '''
    import unittest
    modulenames = '''
        isopydistort.tests.tests
    '''.split()
    suite = unittest.TestSuite()
    loader = unittest.defaultTestLoader
    mobj = None
    for mname in modulenames:
        exec ('import %s as mobj' % mname)
        suite.addTests(loader.loadTestsFromModule(mobj))
    return suite
```

--------------------------------

### Execute unit tests

Source: https://frandsengroup.github.io/isopydistort/tests/index.html

Runs the full test suite and returns a unittest TestResult object.

```python
def test():
    '''Execute all unit tests for the isopydistort package.
    Return a unittest TestResult object.
    '''
    import unittest
    suite = testsuite()
    runner = unittest.TextTestRunner()
    result = runner.run(suite)
    return result
```

--------------------------------

### Download ISODISTORT output

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Submits the final request to the ISODISTORT server and saves the resulting output to a file.

```python
def _postDisplayDistort(data, fname):
    """Download the ISODISTORT output.
    """
    out = requests.post(ISO_FORM_SITE, data=data)
    f = open(fname, 'wb')
    f.write(out.text.encode('utf-8'))
    f.close()
```

--------------------------------

### Full module source code

Source: https://frandsengroup.github.io/isopydistort/tests/index.html

The complete source code for the isopydistort.tests module, including logger initialization and test suite management.

```python
#!/usr/bin/env python
##############################################################################
#
# isopydistort        by Frandsen Group
#                     Benjamin A. Frandsen benfrandsen@byu.edu
#                     (c) 2023 Benjamin Allen Frandsen
#                      All rights reserved
#
# File coded by:    Benjamin Frandsen
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
#
##############################################################################

"""Unit tests for isopydistort.
"""


# create logger instance for the tests subpackage
import logging

logging.basicConfig()
logger = logging.getLogger(__name__)
del logging


def testsuite():
    '''Build a unit tests suite for the isopydistort package.
    Return a unittest.TestSuite object.
    '''
    import unittest
    modulenames = '''
        isopydistort.tests.tests
    '''.split()
    suite = unittest.TestSuite()
    loader = unittest.defaultTestLoader
    mobj = None
    for mname in modulenames:
        exec ('import %s as mobj' % mname)
        suite.addTests(loader.loadTestsFromModule(mobj))
    return suite


def test():
    '''Execute all unit tests for the isopydistort package.
    Return a unittest TestResult object.
    '''
    import unittest
    suite = testsuite()
    runner = unittest.TextTestRunner()
    result = runner.run(suite)
    return result


# End of file
```

--------------------------------

### Define ISODISTORT Output Formats

Source: https://frandsengroup.github.io/isopydistort/isoget.html

List of valid string values for the isoformat parameter to specify the requested output file type.

```text
'isovizdistortion'

'isovizdiffraction'

'structurefile'

'distortionfile'

'domains'

'primary'

'modesdetails'

'completemodesdetails'

'topas'

'fullprof'

'irreps'

'tree'
```

--------------------------------

### Test ISODISTORT connection and retrieval

Source: https://frandsengroup.github.io/isopydistort/tests/tests.html

Verifies connection to the ISODISTORT server and validates the output format of the retrieved data.

```python
class testBasic(unittest.TestCase):
    def test_get(self):
        print('Testing connection to ISODISTORT server...')
        path = os.path.dirname(os.path.abspath(__file__))
        cif = find('hexMnTe.cif',path)
        options = {'basis11':'0', 'basis12':'-1','basis21':'1','basis22':'0'}
        fnameiso = os.path.join(path, "MnTe_iso.txt")
        isopydistort.isoget.get(cif, fnameiso, var_dict=options)
        f = open(fnameiso, 'r')
        lines = f.readlines()
        f.close()
        for idx, line in enumerate(lines):
            if 'mode definitions' in line:
                testIdx = int(1.0*idx)
        teststr = lines[testIdx + 5].strip()[:8]
        self.assertEqual(teststr, 'prm  !a5')
```

```python
def test_get(self):
    print('Testing connection to ISODISTORT server...')
    path = os.path.dirname(os.path.abspath(__file__))
    cif = find('hexMnTe.cif',path)
    options = {'basis11':'0', 'basis12':'-1','basis21':'1','basis22':'0'}
    fnameiso = os.path.join(path, "MnTe_iso.txt")
    isopydistort.isoget.get(cif, fnameiso, var_dict=options)
    f = open(fnameiso, 'r')
    lines = f.readlines()
    f.close()
    for idx, line in enumerate(lines):
        if 'mode definitions' in line:
            testIdx = int(1.0*idx)
    teststr = lines[testIdx + 5].strip()[:8]
    self.assertEqual(teststr, 'prm  !a5')
```

--------------------------------

### Unit test implementation for isopydistort

Source: https://frandsengroup.github.io/isopydistort/tests/tests.html

The test suite verifies the retrieval of ISODISTORT data by comparing output against a known CIF file and expected mode definitions.

```python
#!/usr/bin/env python
##############################################################################
#
# isopydistort        by Frandsen Group
#                     Benjamin A. Frandsen benfrandsen@byu.edu
#                     (c) 2023 Benjamin Allen Frandsen
#                      All rights reserved
#
# File coded by:    Benjamin Frandsen
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
#
##############################################################################

"""Unit tests basic isopydistort functionalities. Execute via
python -m isopydistort.tests.tests
"""

import unittest
import isopydistort
import sys
import os

##############################################################################
def find(name, path):
    for root, dirs, files in os.walk(path):
        if name in files:
            return os.path.join(root, name)

class testBasic(unittest.TestCase):
    def test_get(self):
        print('Testing connection to ISODISTORT server...')
        path = os.path.dirname(os.path.abspath(__file__))
        cif = find('hexMnTe.cif',path)
        options = {'basis11':'0', 'basis12':'-1','basis21':'1','basis22':'0'}
        fnameiso = os.path.join(path, "MnTe_iso.txt")
        isopydistort.isoget.get(cif, fnameiso, var_dict=options)
        f = open(fnameiso, 'r')
        lines = f.readlines()
        f.close()
        for idx, line in enumerate(lines):
            if 'mode definitions' in line:
                testIdx = int(1.0*idx)
        teststr = lines[testIdx + 5].strip()[:8]
        self.assertEqual(teststr, 'prm  !a5')
```

--------------------------------

### Interface with ISODISTORT

Source: https://frandsengroup.github.io/isopydistort/isoget.html

The module uses the requests library to handle file uploads and form submissions to the ISODISTORT web service.

```python
#!/usr/bin/env python
##############################################################################
#
# isopydistort         by Frandsen Group
#                     Benjamin A. Frandsen benfrandsen@byu.edu
#                     (c) 2023 Benjamin Allen Frandsen
#                      All rights reserved
#
# File coded by:    Parker Hamilton, Tobias Bird, Ben Frandsen
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
# We acknowledge Brian Toby and Robert Von Dreele as the first to develop a
# python interface to ISODISTORT, which served as a valuable starting point
# for this package. Their work can be found as part of the GSAS-II software at
# https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/trunk/ISODISTORT.py
##############################################################################

"""Tools to interface with ISODISTORT"""

import requests

ISO_UPLOAD_SITE = "https://iso.byu.edu/iso/isodistortuploadfile.php"
ISO_FORM_SITE = "https://iso.byu.edu/iso/isodistortform.php"


def _uploadCIF(cif):
    """Upload CIF to ISODISTORT.
    """
    f = open(cif, 'rb')
    up = {'toProcess': (cif, f), }
    out = requests.post(ISO_UPLOAD_SITE, files=up).text
    f.close()

    start = out.index("VALUE=")
    start = out.index('"', start + 1) + 1
    end = out.index('"', start)
    fname = out[start:end]

    return fname

def _postParentCIF(fname):
    #posts initially uploaded CIF, sets all data
    up = {'filename': fname, 'input': 'uploadparentcif'}
    out = requests.post(ISO_FORM_SITE, up)
    data = {}
    line_iter = out.iter_lines()

    for line in line_iter:
        if b'INPUT TYPE="hidden"' in line:
            items = line.decode('utf-8').split(' ', 3)
            name = items[2].split('=')[1].strip('"')

            val = items[3].split('=', 1)[1].strip('>"')
            data[name] = val


    return out, data

def _setDatam3(out, data, var_dict = {}, selection = 1):
    """sets necessary data for method 3 - rolls in postIsosubgroup and part of postParentm3"""
    line_iter = out.iter_lines()
    for line in line_iter:
        if b"Method 3" in line:
            break

    for line in line_iter:
        if b'INPUT TYPE="hidden"' in line:
            items = line.decode('utf-8').split(' ', 3)
            name = items[2].split('=')[1].strip('"')

            val = items[3].split('=', 1)[1].strip('>"')
            data[name] = val
        if b'Method 4' in line:
            break

    data['subgroupsym'] = '1 P1 C1-1'
    data['pointgroupsym'] = '0'
    data['latticetype'] = 'direct'
    data['centering'] = 'd'
    data['basis11'] = '1'
    data['basis12'] = '0'
    data['basis13'] = '0'
    data['basis21'] = '0'
    data['basis22'] = '1'
    data['basis23'] = '0'
    data['basis31'] = '0'
    data['basis32'] = '0'
    data['basis33'] = '1'
    for key, value in var_dict.items():
        data[key] = value

    out = requests.post(ISO_FORM_SITE, data=data)
    data = {}
    line_iter = out.iter_lines()

    for line in line_iter:
        if b"<FORM ACTION" in line:
            break

    for line in line_iter:
        if b'INPUT TYPE="hidden"' in line:
            items = line.decode('utf-8').split(' ', 3)
            name = items[2].split('=')[1].strip('"')

            val = items[3].split('=', 1)[1].strip('>"')
            data[name] = val
        if b'<br>' in line:
            break

    counter = 0  # keep track of which distortion we are on
    for line in line_iter:
        if b'RADIO' in line:
            counter += 1
            if counter == selection:  # grab data just for the one we want
                items = line.decode('utf-8').split(' ', 3)
                name = items[2].split('=')[1].strip('"')

                val = items[3].split('=', 1)[1].strip('>"')
                data[name] = val

        if b'</FORM>' in line:
            break

    return data





def _setDatam4(data, subcif, specify = False, basis = [], var_dict = {}):

    subfname = _uploadCIF(subcif)
    data['input'] = 'uploadsubgroupcif'
    data['filename'] = subfname

    out = requests.post(ISO_FORM_SITE, data=data)
    line_iter = out.iter_lines()
    # for line in line_iter:
    # print(line.decode('utf-8'))

    for line in line_iter:
        if b'INPUT TYPE="hidden"' in line:
            items = line.decode('utf-8').split(' ', 3)
            name = items[2].split('=')[1].strip('"')

            val = items[3].split('=', 1)[1].strip('>"')
            data[name] = val
        if specify == False and b'OPTION VALUE=' in line:
            data['inputbasis'] = 'list'
            items = line.decode('utf-8').split(' ', 1)
            data['basisselect'] = items[1].split('=')[1].split(">")[0].strip('"')
            print(items[1].split('=')[1].split(">")[0].strip('"'))

    data['input'] = 'distort'
    data['origintype'] = 'method4'
```

--------------------------------

### Find file in directory tree

Source: https://frandsengroup.github.io/isopydistort/tests/tests.html

Locates a file by name within a specified directory path using os.walk.

```python
def find(name, path):
    for root, dirs, files in os.walk(path):
        if name in files:
            return os.path.join(root, name)
```

--------------------------------

### ISODISTORT Interaction Logic

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Core logic for validating formats and methods before submitting requests to the ISODISTORT server.

```python
### check that the format and method number are acceptable
    formatlist = ['isovizdistortion',
                  'isovizdiffraction',
                  'structurefile',
                  'distortionfile',
                  'domains',
                  'primary',
                  'modesdetails',
                  'completemodesdetails',
                  'topas',
                  'fullprof',
                  'irreps',
                  'tree']
    methodlist = [3,4]

    ### if everything is good, move on to the interaction with ISODISTORT
    if (isoformat in formatlist) and (method in methodlist):
        parentcif = _uploadCIF(cifname)
        out, data = _postParentCIF(parentcif)
        # use the correct post function for the user-supplied method number
        #data = eval('_postParentCIFm' + str(method) + '(parentcif, var_dict)')
        if method == 3:
            data = _setDatam3(out, data, var_dict = var_dict, selection = selection)
        if method == 4:
            data = _setDatam4(data, subcif, specify = specify, basis = basis, var_dict = var_dict)
        #data = _postIsoSubGroup(data, selection)
        data = _postDistort(data, isoformat)
        _postDisplayDistort(data, outfname)
    ### inform the user if there is a problem
    if isoformat not in formatlist:
        print('This is not a valid format. Acceptable options are:\n')
        print('isovizdistortion')
        print('isovizdiffraction')
        print('structurefile')
        print('distortionfile')
        print('domains')
        print('primary')
        print('modesdetails')
        print('completemodesdetails')
        print('topas')
        print('fullprof')
        print('irreps')
        print('tree\n')
        print('Please try again with one of these formats.')
        return
    if method not in methodlist:
        print('This is not a valid method number. Acceptable options are:\n')
        print(methodlist)
        print('Please try again with one of these methods.')
        print('Additional methods may become available in the future.')
        return
```

--------------------------------

### Retrieve distortion modes from ISODISTORT

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Use this function to automate the process of uploading a CIF file and requesting specific distortion data from the ISODISTORT server. Ensure the provided method number and output format are supported by the current API implementation.

```python
def get(cifname, outfname, method=3, var_dict={}, isoformat='topas', selection=1, subcif = "", specify = False, basis = []):
    """Interacts with the ISODISTORT website to get distortion modes.

    Args:
        cifname (str): The name of the local cif file you want to use.
        outfname (str): The name of the file where you want the ISODISTORT
            output saved.
        method (int): Method number to be used by the ISODISTORT server. The
            currently available method numbers are 3 and 4.
        var_dict (dict): Variables to pass to ISODISTORT to set up the
            subgroup symmetry, lattice, and basis. The required dictionary
            keys depend on the method number chosen, as described below.

            Method 3: Keys and default values are given below. It defaults to
            P1 symmetry and an identity matrix for the supercell basis.\n
                'subgroupsym' = '1 P1 C1-1'\n
                'pointgroupsym' = '0'\n
                'latticetype' = 'direct'\n
                'centering' = 'd' (for default)\n
                'basis11' = '1'\n
                'basis12' = '0'\n
                'basis13' = '0'\n
                'basis21' = '0'\n
                'basis22' = '1'\n
                'basis23' = '0'\n
                'basis31' = '0'\n
                'basis32' = '0'\n
                'basis33' = '1'\n
            Note that the 'subgroupsym' value can simply be the space group
            number (as a string) for the desired subgroup. It is not
            recommended to use the space group symbol alone, since this is
            not always read correctly.
        isoformat (str): format of the output file requested from the
            ISODISTORT server. Allowed values are:\n
                'isovizdistortion'\n
                'isovizdiffraction'\n
                'structurefile'\n
                'distortionfile'\n
                'domains'\n
                'primary'\n
                'modesdetails'\n
                'completemodesdetails'\n
                'topas'\n
                'fullprof'\n
                'irreps'\n
                'tree'\n
            See https://stokes.byu.edu/iso/isodistorthelp.php#savedist for
            information about each format.
        selection (int): The number of the desired distortion from the list
            of possible distortions provided by ISODISTORT, starting from 1
            at the top and increasing as you move downward through the list.
            Default value is 1.
    """
    ### check that the format and method number are acceptable
    formatlist = ['isovizdistortion',
                  'isovizdiffraction',
                  'structurefile',
                  'distortionfile',
                  'domains',
                  'primary',
                  'modesdetails',
                  'completemodesdetails',
                  'topas',
                  'fullprof',
                  'irreps',
                  'tree']
    methodlist = [3,4]

    ### if everything is good, move on to the interaction with ISODISTORT
    if (isoformat in formatlist) and (method in methodlist):
        parentcif = _uploadCIF(cifname)
        out, data = _postParentCIF(parentcif)
        # use the correct post function for the user-supplied method number
        #data = eval('_postParentCIFm' + str(method) + '(parentcif, var_dict)')
        if method == 3:
            data = _setDatam3(out, data, var_dict = var_dict, selection = selection)
        if method == 4:
            data = _setDatam4(data, subcif, specify = specify, basis = basis, var_dict = var_dict)
        #data = _postIsoSubGroup(data, selection)
        data = _postDistort(data, isoformat)
        _postDisplayDistort(data, outfname)
    ### inform the user if there is a problem
    if isoformat not in formatlist:
        print('This is not a valid format. Acceptable options are:\n')
        print('isovizdistortion')
        print('isovizdiffraction')
        print('structurefile')
        print('distortionfile')
        print('domains')
        print('primary')
        print('modesdetails')
        print('completemodesdetails')
        print('topas')
        print('fullprof')
        print('irreps')
        print('tree\n')
        print('Please try again with one of these formats.')
        return
    if method not in methodlist:
        print('This is not a valid method number. Acceptable options are:\n')
        print(methodlist)
        print('Please try again with one of these methods.')
        print('Additional methods may become available in the future.')
        return
```

--------------------------------

### Parse ISODISTORT form data

Source: https://frandsengroup.github.io/isopydistort/isoget.html

Processes the HTML response from the ISODISTORT server to extract hidden form fields and current settings.

```python
def _postDistort(data, isoformat):
    """Prepare the data for downloading.
    """
    out = requests.post(ISO_FORM_SITE, data=data)

    data = {}
    line_iter = out.iter_lines()
    for line in line_iter:
        if b"<FORM ACTION" in line:
            break

    for line in line_iter:
        if b'INPUT TYPE="hidden"' in line:
            items = line.decode('utf-8').split(' ', 3)
            name = items[2].split('=')[1].strip('"')

            val = items[3].split('=', 1)[1].strip('>"')
            data[name] = val

        if b'input type="text"' in line:
            items = line.decode('utf-8').split(' ', 5)
            name = [s for s in items if 'name=' in s][0].split('=')[1].strip('"')

            val = [s for s in items if 'value=' in s][0].split('=')[1].strip('"')
            data[name] = val

        if b'RADIO' in line and b'CHECKED' in line:
            items = line.decode('utf-8').split(' ', 3)
            name = items[2].split('"')[1]

            val = items[3].split('"')[1]
            data[name] = val

        if b'</FORM>' in line:
            break

    data['origintype'] = isoformat
    return data
```
Tokens:
Raw