Module isopydistort.isoget

#!/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'

    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



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


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()


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