Module `ctoolkit.SCALEUP.SCALEUP`

Expand source code

from toolkit.global_vars.ext_libs import *
from toolkit.tools import tools
class SCALEUP():
    def __init__(self):
        #self.read_poscar()
        self.tools = tools.tools()
        self.title = 'Toolkit_generated\n'
        self.B = np.zeros([3,3], dtype=float)
        self.SC = np.array([0,0,0], dtype=int)
        self.a_lat = 1.0
        self.nat = 0
        self.names = []
        self.namelist = []
        self.nspecies = 0
        self.atom_id = []
        self.at_type = []
        self.cell_id = []
        self.lattype = '\n'
        self.multiplicity = [0]
        self.volume = 0.0
        self.at_frac = np.array(np.array([.0, .0, .0], dtype=float))
        self.at_cart = np.array(np.array([.0, .0, .0], dtype=float))
        self.type = "SCALEUP"

    def apply_distortion(self):
        strains_B = np.array([[self.strains[0], self.strains[5], self.strains[4]], 
                              [self.strains[5], self.strains[1], self.strains[3]], 
                              [self.strains[4], self.strains[3], self.strains[2]]], dtype=float)
        self.B = np.dot((np.eye(3)+strains_B), self.B)
        for i in range(len(self.at_frac)):
            self.at_cart[i] = np.dot(self.B, self.at_frac[i]) + self.disp[i]
            self.at_frac[i] = self.tools.cart_to_frac(self.B, self.at_cart[i])

    def read_restart_file(self, file):
        lines = open(file, 'r').readlines()
        SF = np.array([float(lines[3].split()[x]) for x in range(6)], dtype=float)
        self.strains = np.array([SF[0], SF[1], SF[2],
                                SF[3], SF[4],SF[5]], dtype=float)
        self.disp = np.zeros([self.nat, 3], dtype=float)
        for i in range(self.nat):
            self.disp[i] = np.array([float(lines[4+i].split()[5+x]) for x in range(3)])

        self.disp = 0.52917721*self.disp

    def read_structure_file(self, file):
        lines = open(file, 'r').readlines()
        self.SC = np.array([float(lines[0].split()[x]) for x in range(3)], dtype=int)
        self.nat = int(lines[1].split()[0])*np.prod(self.SC)
        self.nspecies = int(lines[1].split()[1])
        self.names = lines[2].split()[:]
        self.B = 0.52917721*np.array([[float(lines[3].split()[3*x+y]) for y in range(3)] for x in range(3)], dtype=float)
        self.at_frac = np.zeros([self.nat, 3], dtype=float)
        self.at_cart = np.zeros([self.nat, 3], dtype=float)
        self.cell_id = np.zeros([self.nat, 3], dtype=int)
        self.atom_id = np.zeros([self.nat], dtype=int)
        self.at_type = np.zeros([self.nat], dtype=int)
        self.namelist = []
        self.multiplicity = np.zeros([self.nspecies], dtype=int)
        for i in range(self.nat):
            self.at_cart[i] = 0.52917721*np.array([float(lines[4+i].split()[5+x]) for x in range(3)])
            self.at_frac[i] = self.tools.cart_to_frac(self.B, self.at_cart[i])
            self.cell_id[i] = np.array([int(lines[4+i].split()[0+x]) for x in range(3)], dtype=int)
            self.atom_id[i] = int(lines[4+i].split()[3])-1
            self.at_type[i] = int(lines[4+i].split()[4])-1
            self.namelist.append(self.names[self.at_type[i]])
            self.multiplicity[self.at_type[i]] += 1
        self.at_frac = self.at_frac

    def write_restart_file(self, filename=None):
        
        s = ''

        for a in [self.SC[0], self.SC[1], self.SC[2]]:
            s += "%d " % a            
        s += '\n'
        for a in [self.nat, self.nspecies]:
            s += "%d " % a
        s += '\n'
        for a in self.names:
            s += "%s " % a
        s += '\n'
        s += '%2.6e\t%2.6e\t%2.6e\t%2.6e\t%2.6e\t%2.6e\n' % (
                self.strains[0], self.strains[1], self.strains[2], 
                self.strains[3], self.strains[4], self.strains[5])
        for i in range(len(self.at_frac)):
            s += '%d  %d  %d  %d  %d   %2.6e\t%2.6e\t%2.6e' % (
                    self.cell_id[i,0], self.cell_id[i, 1], self.cell_id[i, 2],
                    self.atom_id[i], self.at_type[i]+1,
                    self.disp[i, 0], self.disp[i, 1], self.disp[i, 2])
            if i < len(self.at_frac)-1:
                s+='\n'

        if filename == None:
            return s
        else:
            with open(filename, 'w') as f:
                f.write(s)

Classes

class SCALEUP

Expand source code

class SCALEUP():
    def __init__(self):
        #self.read_poscar()
        self.tools = tools.tools()
        self.title = 'Toolkit_generated\n'
        self.B = np.zeros([3,3], dtype=float)
        self.SC = np.array([0,0,0], dtype=int)
        self.a_lat = 1.0
        self.nat = 0
        self.names = []
        self.namelist = []
        self.nspecies = 0
        self.atom_id = []
        self.at_type = []
        self.cell_id = []
        self.lattype = '\n'
        self.multiplicity = [0]
        self.volume = 0.0
        self.at_frac = np.array(np.array([.0, .0, .0], dtype=float))
        self.at_cart = np.array(np.array([.0, .0, .0], dtype=float))
        self.type = "SCALEUP"

    def apply_distortion(self):
        strains_B = np.array([[self.strains[0], self.strains[5], self.strains[4]], 
                              [self.strains[5], self.strains[1], self.strains[3]], 
                              [self.strains[4], self.strains[3], self.strains[2]]], dtype=float)
        self.B = np.dot((np.eye(3)+strains_B), self.B)
        for i in range(len(self.at_frac)):
            self.at_cart[i] = np.dot(self.B, self.at_frac[i]) + self.disp[i]
            self.at_frac[i] = self.tools.cart_to_frac(self.B, self.at_cart[i])

    def read_restart_file(self, file):
        lines = open(file, 'r').readlines()
        SF = np.array([float(lines[3].split()[x]) for x in range(6)], dtype=float)
        self.strains = np.array([SF[0], SF[1], SF[2],
                                SF[3], SF[4],SF[5]], dtype=float)
        self.disp = np.zeros([self.nat, 3], dtype=float)
        for i in range(self.nat):
            self.disp[i] = np.array([float(lines[4+i].split()[5+x]) for x in range(3)])

        self.disp = 0.52917721*self.disp

    def read_structure_file(self, file):
        lines = open(file, 'r').readlines()
        self.SC = np.array([float(lines[0].split()[x]) for x in range(3)], dtype=int)
        self.nat = int(lines[1].split()[0])*np.prod(self.SC)
        self.nspecies = int(lines[1].split()[1])
        self.names = lines[2].split()[:]
        self.B = 0.52917721*np.array([[float(lines[3].split()[3*x+y]) for y in range(3)] for x in range(3)], dtype=float)
        self.at_frac = np.zeros([self.nat, 3], dtype=float)
        self.at_cart = np.zeros([self.nat, 3], dtype=float)
        self.cell_id = np.zeros([self.nat, 3], dtype=int)
        self.atom_id = np.zeros([self.nat], dtype=int)
        self.at_type = np.zeros([self.nat], dtype=int)
        self.namelist = []
        self.multiplicity = np.zeros([self.nspecies], dtype=int)
        for i in range(self.nat):
            self.at_cart[i] = 0.52917721*np.array([float(lines[4+i].split()[5+x]) for x in range(3)])
            self.at_frac[i] = self.tools.cart_to_frac(self.B, self.at_cart[i])
            self.cell_id[i] = np.array([int(lines[4+i].split()[0+x]) for x in range(3)], dtype=int)
            self.atom_id[i] = int(lines[4+i].split()[3])-1
            self.at_type[i] = int(lines[4+i].split()[4])-1
            self.namelist.append(self.names[self.at_type[i]])
            self.multiplicity[self.at_type[i]] += 1
        self.at_frac = self.at_frac

    def write_restart_file(self, filename=None):
        
        s = ''

        for a in [self.SC[0], self.SC[1], self.SC[2]]:
            s += "%d " % a            
        s += '\n'
        for a in [self.nat, self.nspecies]:
            s += "%d " % a
        s += '\n'
        for a in self.names:
            s += "%s " % a
        s += '\n'
        s += '%2.6e\t%2.6e\t%2.6e\t%2.6e\t%2.6e\t%2.6e\n' % (
                self.strains[0], self.strains[1], self.strains[2], 
                self.strains[3], self.strains[4], self.strains[5])
        for i in range(len(self.at_frac)):
            s += '%d  %d  %d  %d  %d   %2.6e\t%2.6e\t%2.6e' % (
                    self.cell_id[i,0], self.cell_id[i, 1], self.cell_id[i, 2],
                    self.atom_id[i], self.at_type[i]+1,
                    self.disp[i, 0], self.disp[i, 1], self.disp[i, 2])
            if i < len(self.at_frac)-1:
                s+='\n'

        if filename == None:
            return s
        else:
            with open(filename, 'w') as f:
                f.write(s)

Methods

def apply_distortion(self)

Expand source code

def apply_distortion(self):
    strains_B = np.array([[self.strains[0], self.strains[5], self.strains[4]], 
                          [self.strains[5], self.strains[1], self.strains[3]], 
                          [self.strains[4], self.strains[3], self.strains[2]]], dtype=float)
    self.B = np.dot((np.eye(3)+strains_B), self.B)
    for i in range(len(self.at_frac)):
        self.at_cart[i] = np.dot(self.B, self.at_frac[i]) + self.disp[i]
        self.at_frac[i] = self.tools.cart_to_frac(self.B, self.at_cart[i])

def read_restart_file(self, file)

Expand source code

def read_restart_file(self, file):
    lines = open(file, 'r').readlines()
    SF = np.array([float(lines[3].split()[x]) for x in range(6)], dtype=float)
    self.strains = np.array([SF[0], SF[1], SF[2],
                            SF[3], SF[4],SF[5]], dtype=float)
    self.disp = np.zeros([self.nat, 3], dtype=float)
    for i in range(self.nat):
        self.disp[i] = np.array([float(lines[4+i].split()[5+x]) for x in range(3)])

    self.disp = 0.52917721*self.disp

def read_structure_file(self, file)

Expand source code

def read_structure_file(self, file):
    lines = open(file, 'r').readlines()
    self.SC = np.array([float(lines[0].split()[x]) for x in range(3)], dtype=int)
    self.nat = int(lines[1].split()[0])*np.prod(self.SC)
    self.nspecies = int(lines[1].split()[1])
    self.names = lines[2].split()[:]
    self.B = 0.52917721*np.array([[float(lines[3].split()[3*x+y]) for y in range(3)] for x in range(3)], dtype=float)
    self.at_frac = np.zeros([self.nat, 3], dtype=float)
    self.at_cart = np.zeros([self.nat, 3], dtype=float)
    self.cell_id = np.zeros([self.nat, 3], dtype=int)
    self.atom_id = np.zeros([self.nat], dtype=int)
    self.at_type = np.zeros([self.nat], dtype=int)
    self.namelist = []
    self.multiplicity = np.zeros([self.nspecies], dtype=int)
    for i in range(self.nat):
        self.at_cart[i] = 0.52917721*np.array([float(lines[4+i].split()[5+x]) for x in range(3)])
        self.at_frac[i] = self.tools.cart_to_frac(self.B, self.at_cart[i])
        self.cell_id[i] = np.array([int(lines[4+i].split()[0+x]) for x in range(3)], dtype=int)
        self.atom_id[i] = int(lines[4+i].split()[3])-1
        self.at_type[i] = int(lines[4+i].split()[4])-1
        self.namelist.append(self.names[self.at_type[i]])
        self.multiplicity[self.at_type[i]] += 1
    self.at_frac = self.at_frac

def write_restart_file(self, filename=None)

Expand source code

def write_restart_file(self, filename=None):
    
    s = ''

    for a in [self.SC[0], self.SC[1], self.SC[2]]:
        s += "%d " % a            
    s += '\n'
    for a in [self.nat, self.nspecies]:
        s += "%d " % a
    s += '\n'
    for a in self.names:
        s += "%s " % a
    s += '\n'
    s += '%2.6e\t%2.6e\t%2.6e\t%2.6e\t%2.6e\t%2.6e\n' % (
            self.strains[0], self.strains[1], self.strains[2], 
            self.strains[3], self.strains[4], self.strains[5])
    for i in range(len(self.at_frac)):
        s += '%d  %d  %d  %d  %d   %2.6e\t%2.6e\t%2.6e' % (
                self.cell_id[i,0], self.cell_id[i, 1], self.cell_id[i, 2],
                self.atom_id[i], self.at_type[i]+1,
                self.disp[i, 0], self.disp[i, 1], self.disp[i, 2])
        if i < len(self.at_frac)-1:
            s+='\n'

    if filename == None:
        return s
    else:
        with open(filename, 'w') as f:
            f.write(s)