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How to use from_parameters method in avocado

Best Python code snippet using avocado_python

creator.py

Source:creator.py

...25    POTCAR_maker.writer(path_to_calc, elem_list)26def undeformed_lattice(a, b, c, alpha, beta, gamma):27    """Creates all necessary files to run a VASP job for initial undeformed structure"""28    calculation_type = "undeformed"29    new_lattice = Lattice.from_parameters(a, b, c, alpha, beta, gamma)30    single_run(calculation_type, new_lattice)31def applied_field(a, b, c, alpha, beta, gamma):32    """Creates all necessary files to run a VASP job for structure33    under applied field (value of the field is set in INCAR_maker)"""34    calculation_type = "Applied_Field"35    new_lattice = Lattice.from_parameters(a, b, c, alpha, beta, gamma)36    single_run(calculation_type, new_lattice)37def volumetric_deformation(n, a, b, c, alpha, beta, gamma):38    """Takes lattice parameters and scales all of them by deformation factor39    Prepares both compressed and expanded structures"""40    V_inc = 'V_' + str(1+n)41    V_dec = 'V_' + str(1-n)42    deformation_types = [V_dec, V_inc]43    for deformation_type in deformation_types:44        if deformation_type == V_dec:45            new_lattice = Lattice.from_parameters(a, b, c, alpha, beta, gamma)46            volume_before = new_lattice.volume47            new_lattice = new_lattice.scale((1 - n) * volume_before)48            single_run(deformation_type, new_lattice)49        if deformation_type == V_inc:50            new_lattice = Lattice.from_parameters(a, b, c, alpha, beta, gamma)51            volume_before = new_lattice.volume52            new_lattice = new_lattice.scale((1 + n) * volume_before)53            single_run(deformation_type, new_lattice)54def uniaxial_defromations(lattice_type, n, a, b, c, alpha, beta, gamma):55    """Takes lattice type as argument and depending on symmetry creates all necessary files to run VASP jobs for all56    possible independent deformations.57    Depending on symmetry create a 3x3 deformation matrix which determines weather a, b, c are deformed. This matrix is58    later passed to POSCAR_maker where it is used for adjusting the lattice matrix.59    Deformations are done both for increase and decrease of each lattice parameter.60    """61    # deformation factor 0.05 == 5%, deformation is done both for expansion and contraction.62    # creating names for deformations:63    a_inc = 'a_' + str(1+n)64    a_dec = 'a_' + str(1-n)65    b_inc = 'b_' + str(1+n)66    b_dec = 'b_' + str(1-n)67    c_inc = 'c_' + str(1+n)68    c_dec = 'c_' + str(1-n)69    if lattice_type == "cubic":70        deformation_types = [a_dec, a_inc]71        for deformation_type in deformation_types:72            if deformation_type == a_dec:73                a_d = a * pow((1 - n), (1/3))74                b_d = b * pow((1 - n), (1/3))75                c_d = c * pow((1 - n), (1/3))76                new_lattice = Lattice.from_parameters(a_d, b_d, c_d, alpha, beta, gamma)77                single_run(deformation_type, new_lattice)78            if deformation_type == a_inc:79                a_i = a * pow((1 + n), (1/3))80                b_i = b * pow((1 + n), (1/3))81                c_i = c * pow((1 + n), (1/3))82                new_lattice = Lattice.from_parameters(a_i, b_i, c_i, alpha, beta, gamma)83                single_run(deformation_type, new_lattice)84    elif lattice_type == "hexagonal":85        deformation_types = [a_dec, a_inc, c_inc, c_dec]86        for deformation_type in deformation_types:87            if deformation_type == a_dec:88                a_d = a * pow((1 - n), (1/2))89                b_d = b * pow((1 - n), (1/2))90                new_lattice = Lattice.from_parameters(a_d, b_d, c, alpha, beta, gamma)91                single_run(deformation_type, new_lattice)92            if deformation_type == c_dec:93                c_d = c * (1 - n)94                new_lattice = Lattice.from_parameters(a, b, c_d, alpha, beta, gamma)95                single_run(deformation_type, new_lattice)96            if deformation_type == a_inc:97                a_i = a * pow((1 + n), (1/2))98                b_i = b * pow((1 + n), (1/2))99                new_lattice = Lattice.from_parameters(a_i, b_i, c, alpha, beta, gamma)100                single_run(deformation_type, new_lattice)101            if deformation_type == c_inc:102                c_i = c * (1 + n)103                new_lattice = Lattice.from_parameters(a, b, c_i, alpha, beta, gamma)104                single_run(deformation_type, new_lattice)105    elif lattice_type == "rhombohedral":106        deformation_types = [a_dec, a_inc]107        for deformation_type in deformation_types:108            if deformation_type == a_dec:109                a_d = a * pow((1 - n), (1/3))110                b_d = b * pow((1 - n), (1/3))111                c_d = c * pow((1 - n), (1/3))112                new_lattice = Lattice.from_parameters(a_d, b_d, c_d, alpha, beta, gamma)113                single_run(deformation_type, new_lattice)114            if deformation_type == a_inc:115                a_i = a * pow((1 + n), (1/3))116                b_i = b * pow((1 + n), (1/3))117                c_i = c * pow((1 + n), (1/3))118                new_lattice = Lattice.from_parameters(a_i, b_i, c_i, alpha, beta, gamma)119                single_run(deformation_type, new_lattice)120    elif lattice_type == "tetragonal":121        deformation_types = [a_dec, a_inc, c_inc, c_dec]122        for deformation_type in deformation_types:123            if deformation_type == a_dec:124                a_d = a * pow((1 - n), (1/2))125                b_d = b * pow((1 - n), (1/2))126                new_lattice = Lattice.from_parameters(a_d, b_d, c, alpha, beta, gamma)127                single_run(deformation_type, new_lattice)128            if deformation_type == c_dec:129                c_d = c * (1 - n)130                new_lattice = Lattice.from_parameters(a, b, c_d, alpha, beta, gamma)131                single_run(deformation_type, new_lattice)132            if deformation_type == a_inc:133                a_i = a * pow((1 + n), (1/2))134                b_i = b * pow((1 + n), (1/2))135                new_lattice = Lattice.from_parameters(a_i, b_i, c, alpha, beta, gamma)136                single_run(deformation_type, new_lattice)137            if deformation_type == c_inc:138                c_i = c * (1 + n)139                new_lattice = Lattice.from_parameters(a, b, c_i, alpha, beta, gamma)140                single_run(deformation_type, new_lattice)141    elif lattice_type == "orthorhombic":142        deformation_types = [a_dec, b_dec, c_dec, a_inc, b_inc, c_inc]143        for deformation_type in deformation_types:144            if deformation_type == a_dec:145                a_d = a * (1 - n)146                new_lattice = Lattice.from_parameters(a_d, b, c, alpha, beta, gamma)147                single_run(deformation_type, new_lattice)148            if deformation_type == b_dec:149                b_d = b * (1 - n)150                new_lattice = Lattice.from_parameters(a, b_d, c, alpha, beta, gamma)151                single_run(deformation_type, new_lattice)152            if deformation_type == c_dec:153                c_d = c * (1 - n)154                new_lattice = Lattice.from_parameters(a, b, c_d, alpha, beta, gamma)155                single_run(deformation_type, new_lattice)156            if deformation_type == a_inc:157                a_i = a * (1 + n)158                new_lattice = Lattice.from_parameters(a_i, b, c, alpha, beta, gamma)159                single_run(deformation_type, new_lattice)160            if deformation_type == b_inc:161                b_i = b * (1 + n)162                new_lattice = Lattice.from_parameters(a, b_i, c, alpha, beta, gamma)163                single_run(deformation_type, new_lattice)164            if deformation_type == c_inc:165                c_i = c * (1 + n)166                new_lattice = Lattice.from_parameters(a, b, c_i, alpha, beta, gamma)167                single_run(deformation_type, new_lattice)168    elif lattice_type == "monoclinic":169        deformation_types = [a_dec, b_dec, c_dec, a_inc, b_inc, c_inc]170        for deformation_type in deformation_types:171            if deformation_type == a_dec:172                a_d = a * (1 - n)173                new_lattice = Lattice.from_parameters(a_d, b, c, alpha, beta, gamma)174                single_run(deformation_type, new_lattice)175            if deformation_type == b_dec:176                b_d = b * (1 - n)177                new_lattice = Lattice.from_parameters(a, b_d, c, alpha, beta, gamma)178                single_run(deformation_type, new_lattice)179            if deformation_type == c_dec:180                c_d = c * (1 - n)181                new_lattice = Lattice.from_parameters(a, b, c_d, alpha, beta, gamma)182                single_run(deformation_type, new_lattice)183            if deformation_type == a_inc:184                a_i = a * (1 + n)185                new_lattice = Lattice.from_parameters(a_i, b, c, alpha, beta, gamma)186                single_run(deformation_type, new_lattice)187            if deformation_type == b_inc:188                b_i = b * (1 + n)189                new_lattice = Lattice.from_parameters(a, b_i, c, alpha, beta, gamma)190                single_run(deformation_type, new_lattice)191            if deformation_type == c_inc:192                c_i = c * (1 + n)193                new_lattice = Lattice.from_parameters(a, b, c_i, alpha, beta, gamma)194                single_run(deformation_type, new_lattice)195    elif lattice_type == "triclinic":196        deformation_types = [a_dec, b_dec, c_dec, a_inc, b_inc, c_inc]197        for deformation_type in deformation_types:198            if deformation_type == a_dec:199                a_d = a * (1 - n)200                new_lattice = Lattice.from_parameters(a_d, b, c, alpha, beta, gamma)201                single_run(deformation_type, new_lattice)202            if deformation_type == b_dec:203                b_d = b * (1 - n)204                new_lattice = Lattice.from_parameters(a, b_d, c, alpha, beta, gamma)205                single_run(deformation_type, new_lattice)206            if deformation_type == c_dec:207                c_d = c * (1 - n)208                new_lattice = Lattice.from_parameters(a, b, c_d, alpha, beta, gamma)209                single_run(deformation_type, new_lattice)210            if deformation_type == a_inc:211                a_i = a * (1 + n)212                new_lattice = Lattice.from_parameters(a_i, b, c, alpha, beta, gamma)213                single_run(deformation_type, new_lattice)214            if deformation_type == b_inc:215                b_i = b * (1 + n)216                new_lattice = Lattice.from_parameters(a, b_i, c, alpha, beta, gamma)217                single_run(deformation_type, new_lattice)218            if deformation_type == c_inc:219                c_i = c * (1 + n)220                new_lattice = Lattice.from_parameters(a, b, c_i, alpha, beta, gamma)221                single_run(deformation_type, new_lattice)222def creator(datalist, datadir, def_factor=0.05, undeformed=True, hydrostatic=False, uniaxial=False, field=False):223    df = pd.read_csv(datalist, index_col=0, sep=',')224    with tqdm.tqdm(total=len(df.index)) as pbar:  # A wrapper that creates nice progress bar225        pbar.set_description("Processing datalist")226        for item in df.index.tolist():227            pbar.update(1)228            ID = str(item)229            global path230            path = output_path + '/' + str(ID) + '/'  # Prepare folder single ID (all subfolders will go there)231            if os.path.exists(path):  # !WARNING! Overwrites existing path!232                shutil.rmtree(path)  #233            os.makedirs(path)  #234            # Take all information from poscar as list of strings:...

latt.py

Source:latt.py

...49    def vc(self):50        return self._c5152    @classmethod53    def from_parameters(cls, a, b, c, alpha, beta, gamma):54        """55        Construct a new Lattice object from parameters.56        Args:57            a:58            b:59            c:60            alpha:61            beta:62            gamma:6364        Returns:6566        """67        angles_r = np.radians([alpha, beta, gamma])68        cos_alpha, cos_beta, cos_gamma = np.cos(angles_r)69        sin_alpha, sin_beta, sin_gamma = np.sin(angles_r)70        val = cls._abs_cap((cos_alpha * cos_beta - cos_gamma) / (sin_alpha * sin_beta))71        va = [a * sin_beta, 0.0, a * cos_beta]72        vb = [-b * sin_alpha * np.cos(np.arccos(val)),73              b * sin_alpha * np.sin(np.arccos(val)), b * cos_alpha]74        vc = [0.0, 0.0, float(c)]75        return cls(np.asarray([va, vb, vc]))7677    @staticmethod78    def _abs_cap(val, max_abs_val=1):79        """80        Return the value with its absolute value capped at max_abs_val.8182        Particularly useful in passing values to trignometric functions where83        numerical errors may result in an argument > 1 being passed in.8485        Args:8687            val (float): Input value.8889            max_abs_val (float): The maximum absolute value for val. Defaults to 1.9091        Returns:92            val if abs(val) < 1 else sign of val * max_abs_val.93        """94        return max(min(val, max_abs_val), -max_abs_val)9596    @classmethod97    def cubic(cls, a):98        """Construct cubic Lattice from lattice parameter information."""99        return cls.from_parameters(a, a, a, 90, 90, 90)100101    @classmethod102    def tetragonal(cls, a, c):103        """Construct tetragonal Lattice from lattice parameter information."""104        return cls.from_parameters(a, a, c, 90, 90, 90)105106    @classmethod107    def orthorhombic(cls, a, b, c):108        """Construct orthorhombic Lattice."""109        return cls.from_parameters(a, b, c, 90, 90, 90)110111    @classmethod112    def monoclinic(cls, a, b, c, beta):113        """Construct monoclinic Lattice from lattice parameter information."""114        return cls.from_parameters(a, b, c, 90, beta, 90)115116    @classmethod117    def hexagonal(cls, a, c):118        """Construct hexagonal Lattice from lattice parameter information."""119        return cls.from_parameters(a, a, c, 90, 90, 120)120121    @classmethod122    def rhombohedral(cls, a, alpha):123        """Construct rhombohedral Lattice."""124        return cls.from_parameters(a, a, a, alpha, alpha, alpha)125126    @property127    def lattice(self):128        """129130        Returns:  lattice matrix.131132        """133        return self._lat134135    def inv_lattice(self):136        """137138        Returns: inverse lattice matrix.
...

message_back.py

Source:message_back.py

1#!/usr/bin/env python2# -*- coding: utf-8 -*-3import os4from flask import Flask, Response, request5import simplejson as json6import plivoxml7import plivo8PLIVO_AUTH_ID = "MANTLJODIXMTJKNJDMYJ"9PLIVO_AUTH_TOKEN = "MWY5MzIxNjAyYWUzOTc1MjZjMDViNDYxNTAwYTFh"10plivo_number = "14154290712"11data = []12app = Flask(__name__)13@app.route('/response/message_back/', methods=['GET', 'POST'])14def message_back():15    if request.method == 'POST':16        print request.form17        from_num = request.form.get('From')18        from_parameters = request.form.get('Text')19        from_parameters = from_parameters.strip().split()20        print from_parameters21        person = {}22        person['phone_num'] = long(from_num)23        person['country_code'] = from_parameters[0]24        person['pregancy_stage'] = int(from_parameters[1])25        person['has_smartphone'] = False 26        person['language'] = 'english'27        person['responsiveness'] = 528        29        add_person(person)30        31        subscriber_msg = "You are now subscribed to the feed"32        message_params = {33            'src':plivo_number,34            'dst':from_num,35            'text':subscriber_msg,36        }37        p = plivo.RestAPI(PLIVO_AUTH_ID, PLIVO_AUTH_TOKEN)38        res = p.send_message(message_params)39        return str(res)40        41        42@app.route('/subscribers/', methods=['GET'])43def get_subscriber():44    global data45    read_data()46    country_code = request.args.get('country_code')47    if country_code == None:48        return Response( json.dumps(data),  mimetype="application/json")     49    else:50        return_data = filter(lambda x: x['country_code'] == country_code, data)51        return Response( json.dumps(return_data),  mimetype="application/json")     52        53def save_data():54    global data55    with open('subscribers.txt', 'w') as fp:56        json.dump(data, fp)57        58def read_data():59    global data60    with open("subscribers.txt", 'r') as fp:61        data = json.load(fp)  62def add_person(person_dict):63    print person_dict64    global data65    read_data()66    data.append(person_dict)67    save_data()68if __name__ == '__main__':...

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