def action(index, folder):
ax = axs[0]
gap= axs[1]
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
import pyramids.plot.PlotUtility as pu
pu.plot2DBZ(ax,atoms)
pu.plot2DBZ(gap,atoms)
eigSteps = dp.getEIGSteps()
initStep, finalStep = eigSteps[0],eigSteps[-1]
print initStep, finalStep
energy = dp.readEigFile('siesta'+str(finalStep)+'.EIG')
popStart = dp.readEigFile('siesta'+str(finalStep)+'q.EIG')
popEnd = dp.readEigFile('siesta'+str(initStep)+'q.EIG')
part = np.abs(popStart - popEnd)
plotted = part[:,3]
plotted[plotted < 0.1*np.max(plotted)] = 0.0
norm = 100.0
kcoor, kweight = dp.readKpoints()
kcoorAll, klistAll = dp.recoverAllKPoints(kcoor,2*np.pi*atoms.get_reciprocal_cell(),
repeat = [1,1,0], flatten = False)
diffEnergy = energy[:,4] - energy[:,3]
outRange = np.ones(diffEnergy.shape)*20
outRange[diffEnergy > 4.5] = 0.0
for k in kcoorAll:
ct1 = ax.scatter(k[:,0], k[:,1], norm*plotted, color = colors[index], marker='h',
alpha=1.0, lw=0.0)
ct2 = gap.scatter(k[:,0], k[:,1], outRange, cmap=cmap, c=diffEnergy,
vmin = 1.0, vmax = 5.0, marker='h', alpha=1.0, lw=0.00)
ax.scatter([], [], 60, color = colors[index], label=folder, alpha=1.0, lw=0.0)
if index ==0 :
#plt.colorbar(ct2,ax=ax,extendrect=False)
plt.colorbar(ct2,ax=gap,extendrect=False)
def action(index, folder):
ax = axs[0]
gap = axs[1]
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
import pyramids.plot.PlotUtility as pu
pu.plot2DBZ(ax, atoms)
pu.plot2DBZ(gap, atoms)
eigSteps = dp.getEIGSteps()
initStep, finalStep = eigSteps[0], eigSteps[-1]
print initStep, finalStep
energy = dp.readEigFile('siesta' + str(finalStep) + '.EIG')
popStart = dp.readEigFile('siesta' + str(finalStep) + 'q.EIG')
popEnd = dp.readEigFile('siesta' + str(initStep) + 'q.EIG')
part = np.abs(popStart - popEnd)
plotted = part[:, 3]
plotted[plotted < 0.1 * np.max(plotted)] = 0.0
norm = 100.0
kcoor, kweight = dp.readKpoints()
kcoorAll, klistAll = dp.recoverAllKPoints(kcoor,
2 * np.pi *
atoms.get_reciprocal_cell(),
repeat=[1, 1, 0],
flatten=False)
diffEnergy = energy[:, 4] - energy[:, 3]
outRange = np.ones(diffEnergy.shape) * 20
outRange[diffEnergy > 4.5] = 0.0
for k in kcoorAll:
ct1 = ax.scatter(k[:, 0],
k[:, 1],
norm * plotted,
color=colors[index],
marker='h',
alpha=1.0,
lw=0.0)
ct2 = gap.scatter(k[:, 0],
k[:, 1],
outRange,
cmap=cmap,
c=diffEnergy,
vmin=1.0,
vmax=5.0,
marker='h',
alpha=1.0,
lw=0.00)
ax.scatter([], [],
60,
color=colors[index],
label=folder,
alpha=1.0,
lw=0.0)
if index == 0:
#plt.colorbar(ct2,ax=ax,extendrect=False)
plt.colorbar(ct2, ax=gap, extendrect=False)
def getStructrue():
if os.path.exists('structure.vasp'):
from ase.io import read
atoms = read('structure.vasp', format='vasp')
#import ase.build
#ase.build.niggli_reduce(atoms)
elif os.path.exists('siesta.XV'):
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
return atoms
def getStructrue():
if os.path.exists('structure.vasp'):
from ase.io import read
atoms = read('structure.vasp',format='vasp')
#import ase.build
#ase.build.niggli_reduce(atoms)
elif os.path.exists('siesta.XV'):
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
return atoms
def read(self, filename):
"""Read structural parameters from file .XV file
Read other results from other files
filename : siesta.XV
"""
fname = self.getpath(filename)
if not os.path.exists(fname):
raise ReadError("The restart file '%s' does not exist" % fname)
self.atoms = xv_to_atoms(fname)
self.read_results()
def read_structure(self, structfile):
# returns ase structure from proper structure file
structure = ""
if self.calculator == "VASP":
structure = read_vasp(
structfile) # structure - instance of ASE.Atom class
if self.calculator == "siesta":
structure = xv_to_atoms(structfile)
if self.calculator == "openmx": # hashfile of openmx.dat (openmx.dat#)
pos, species, cell = read_openmx_hashfile(structfile)
structure = Atoms(species)
structure.set_positions(pos)
structure.set_cell(cell)
return structure
def action(index, folder):
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
import pyramids.plot.PlotUtility as pu
pu.plot2DBZ(ax,atoms)
eigSteps = dp.getEIGSteps()
initStep, finalStep = eigSteps[0],eigSteps[-1]
#eigenvalue = dp.readEigFile('siesta'+str(finalStep)+'.EIG')
part = np.abs(dp.readEigFile('siesta'+str(finalStep)+'q.EIG') - dp.readEigFile('siesta'+str(initStep)+'q.EIG'))
norm = 100.0/max(part[:,3])
kcoor, kweight = dp.readKpoints()
kcoorAll, klistAll = dp.recoverAllKPoints(kcoor,2*np.pi*atoms.get_reciprocal_cell(),repeat = [1,1,0])
#evolvingBands = range(3,5)
ax.scatter(kcoorAll[:,0], kcoorAll[:,1], s=norm*np.abs(part[:,3]),lw=0.0, color= color[index], label=folder)
def generateStructPNG(atoms=None, rotation=[0,0,0],camera='perspective',repeat = [1,1,1], cell=False,**args):
from ase.calculators.siesta.import_functions import xv_to_atoms
from ase.io import write
if atoms is None:
atoms = xv_to_atoms('siesta.XV')
rot = str(rotation[0])+'x,'+str(rotation[1])+'y,'+str(rotation[2])+'z'
if cell:
showcell = 2
else:
showcell = 0
kwargs = {
'rotation' : rot, # text string with rotation (default='' )
'radii' : 1.0, # float, or a list with one float per atom
'colors' : None,# List: one (r, g, b) tuple per atom
'show_unit_cell': showcell, # 0, 1, or 2 to not show, show, and show all of cell
}
kwargs.update({
'run_povray' : True, # Run povray or just write .pov + .ini files
'display' : False,# Display while rendering
'pause' : True, # Pause when done rendering (only if display)
'transparent' : True,# Transparent background
'canvas_width' : None, # Width of canvas in pixels
'canvas_height': 800, # Height of canvas in pixels
'camera_dist' : 12000., # Distance from camera to front atom
'image_plane' : 0, # Distance from front atom to image plane
'camera_type' : camera, # perspective, ultra_wide_angle, orthographic
'point_lights' : [], # [[loc1, color1], [loc2, color2],...]
'area_light' : [(2., 3., 40.), # location
'White', # color
.7, .7, 3, 3], # width, height, Nlamps_x, Nlamps_y
'background' : 'White', # color
'textures' : None, # Length of atoms list of texture names
'celllinewidth': 0.1, # Radius of the cylinders representing the cell
})
cell = atoms.cell
atoms.center()
atoms = atoms*repeat
for position in atoms.positions:
position -= repeat[0]/2*cell[0,:]
position -= repeat[1]/2*cell[1,:]
position -= repeat[2]/2*cell[2,:]
atoms.cell = cell
write('struct.pov',atoms, **kwargs)
def getTrajactory():
options = tdapOptions()
#print(options.laserParam)
systemLabel = options.label
NumBlocks = int(
os.popen('grep -i %s %s.MD_CAR | wc -l' %
(systemLabel, systemLabel)).readline().split()[0])
position_file = open(systemLabel + '.MD_CAR')
atomNumList = [
int(i)
for i in os.popen('head -6 siesta.MD_CAR |tail -1').readline().split()
]
numAtomPositionLine = sum(atomNumList)
totalNumLine = numAtomPositionLine + 7
context = position_file.readlines()
#import ase.calculators.vasp as vinter
#from ase.visualize import view
atoms = xv_to_atoms(systemLabel + '.XV')
atoms.pbc = [True, True, True]
filename = 'Trajectory'
from ase.io.trajectory import Trajectory
if not os.path.exists(filename) or os.path.getmtime(
filename) < os.path.getmtime(systemLabel + '.MD_CAR'):
atomsList = []
for index in range(NumBlocks):
output = context[index * totalNumLine:(index + 1) * totalNumLine]
coodinates = np.array(
[[float(value.replace('\n', '')) for value in line.split()]
for line in output[7:]])
atomsCurrent = atoms.copy()
atomsCurrent.set_scaled_positions(coodinates)
atomsList.append(atomsCurrent)
#poscarFileName = "POSCAR"+str(index)
#poscarFile=open(poscarFileName,'w')
#poscarFile.writelines(output)
from ase.io import write
write(filename, atomsList, 'traj')
atomsList = Trajectory(filename)
#print atomsList
return atomsList
def getTrajactory():
options = tdapOptions()
systemLabel = options.label
NumBlocks=int(os.popen('grep -i '+systemLabel+' '+systemLabel+'.MD_CAR | wc -l').readline().split()[0])
position_file = open(systemLabel+'.MD_CAR')
atomNumList = [int(i) for i in os.popen('head -6 siesta.MD_CAR |tail -1').readline().split()]
numAtomPositionLine = sum(atomNumList)
totalNumLine = numAtomPositionLine + 7
context = position_file.readlines()
from ase.calculators.siesta.import_functions import xv_to_atoms
#import ase.calculators.vasp as vinter
#from ase.visualize import view
atoms = xv_to_atoms(systemLabel+'.XV')
atoms.pbc = [True,True,True]
filename = 'Trajectory'
from ase.io.trajectory import Trajectory
if not os.path.exists(filename) or os.path.getmtime(filename) < os.path.getmtime(systemLabel+'.MD_CAR'):
atomsList = []
for index in range(NumBlocks):
output=context[index*totalNumLine:(index+1)*totalNumLine]
coodinates=np.array([[float(value.replace('\n',''))
for value in line.split()]
for line in output[7:]])
atomsCurrent = atoms.copy()
atomsCurrent.set_scaled_positions(coodinates)
atomsList.append(atomsCurrent)
#poscarFileName = "POSCAR"+str(index)
#poscarFile=open(poscarFileName,'w')
#poscarFile.writelines(output)
from ase.io import write
write(filename,atomsList,'traj')
atomsList = Trajectory(filename)
#print atomsList
return atomsList
def action(index, folder):
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
import pyramids.plot.PlotUtility as pu
pu.plot2DBZ(ax, atoms)
eigSteps = dp.getEIGSteps()
initStep, finalStep = eigSteps[0], eigSteps[-1]
#eigenvalue = dp.readEigFile('siesta'+str(finalStep)+'.EIG')
part = np.abs(
dp.readEigFile('siesta' + str(finalStep) + 'q.EIG') -
dp.readEigFile('siesta' + str(initStep) + 'q.EIG'))
norm = 100.0 / max(part[:, 3])
kcoor, kweight = dp.readKpoints()
kcoorAll, klistAll = dp.recoverAllKPoints(kcoor,
2 * np.pi *
atoms.get_reciprocal_cell(),
repeat=[1, 1, 0])
#evolvingBands = range(3,5)
ax.scatter(kcoorAll[:, 0],
kcoorAll[:, 1],
s=norm * np.abs(part[:, 3]),
lw=0.0,
color=color[index],
label=folder)
def read(self, filename):
"""Read parameters from file."""
if not os.path.exists(filename):
raise ReadError("The restart file '%s' does not exist" % filename)
self.atoms = xv_to_atoms(filename)
self.read_results()
def read(self, filename):
"""Read parameters from file."""
if not os.path.exists(filename):
raise ReadError("The restart file '%s' does not exist" % filename)
self.atoms = xv_to_atoms(filename)
self.read_results()
#kargs = ma.getPropertyFromPosition(ylabel=r'', xlabel=r'$A \sin\theta$',title='')
#ma.setProperty(ax,**kargs)
#
#plt.tight_layout()
#SaveName = __file__.split('/')[-1].split('.')[0]
#for save_type in ['.pdf']:
# plt.savefig(SaveName+save_type,transparent=True,dpi=600)
import ase.dft.kpoints as adk
from ase.calculators.siesta.import_functions import xv_to_atoms
from ase.visualize import view
from graphene import *
import pyramids.plot.PlotUtility as pu
atoms = xv_to_atoms('siesta.XV')
#view(atoms)
reciprocal_vectors = 2*np.pi*atoms.get_reciprocal_cell()
N = 24
mesh = adk.monkhorst_pack([N ,N ,1])+ np.array([0.5/N , 0.5/N , 0.0])
shiftK = np.array([1/3.0 , 2/3.0, 0.0]).dot(reciprocal_vectors)
kpoints = mesh.dot(reciprocal_vectors)[:,:2]/3.0
args={'t0':10.0,'sigma': 4.0, 'omega':2.0, 'phi':0.0, 'parity':1, 'vFermi' : 6.348}
args['A'] = 0.2
args['times'] = np.linspace(0.0, 20.0, 100.0)
energyBandDown = []
energyBandUp = []
#!/usr/bin/python
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dP
import pyramids.plot.setting as ma
import pyramids.plot.PlotUtility as pu
from ase.dft.kpoints import get_special_points
from ase.calculators.siesta.import_functions import xv_to_atoms
from ase.lattice import hexagonal
#------------------------------------------------------------------------------
kpath = []
cut = [0]
atom = xv_to_atoms('siesta.XV')
specialKPoints = [r'$M$', r'$\Gamma$', r'$K$', r'$M$']
kpoints, kwgt = dP.readKpoints()
nkpts = kpoints.shape[0]
for i in range(79, 2, -13):
print i
kpath.append(i)
cut.append(len(kpath))
kpath.append(6)
kpath.append(5)
for i in range(12, 45, 11):
print i
kpath.append(i)
kpath.append(i - 1)
"""
Created on Mon Mar 21 12:31:44 2016
@author: cl-iop
"""
import numpy as np
from scipy.fftpack import fft, ifft
from pyramids.plot.setting import getPropertyFromPosition, setProperty, getColors
from pyramids.io.fdf import tdapOptions
import pyramids.io.result as dp
import matplotlib.pyplot as plt
import os
import ase
from ase.calculators.siesta.import_functions import xv_to_atoms
atom_temp = xv_to_atoms('siesta.XV')
atoms = ase.atoms.Atoms(symbols=atom_temp.get_chemical_symbols(),
positions=atom_temp.get_positions(),
cell = atom_temp.get_cell())
reciprocal_vectors = 2*np.pi*atoms.get_reciprocal_cell()
kcoor, kweight = dp.readKpoints()
import matplotlib.pyplot as plt
cut = 1
fig = plt.figure()
from mpl_toolkits.mplot3d import Axes3D
ax = fig.add_subplot(1,1,1,projection='3d')
points=np.array([(reciprocal_vectors[0,0:2]*i+
def get_best_individual(self,
out="Individuals",
calculator="VASP",
mode="2D"):
# returns e_tot/atom of best individual, mode="2D" or "all", uses Individuals file
# deprecated
outfile = open(out, "r")
e_tot_min = 0.
indx_min = 0
indx_pop = 1
indx_pop_min = 1
for line in outfile:
test = line.find("data of pop:")
if test > -1:
line_sp = line.split()
pop = str(line_sp[3])
pop = pop.replace('POP', '')
indx_pop = int(pop)
# print(indx_pop)
test = line.find("individual ")
if test > -1:
line_sp = line.split()
e_tot = float(line_sp[4])
tmp = str(line_sp[2])
tmp = tmp.replace(':', '')
indx = int(tmp)
if mode == "all":
if e_tot < e_tot_min:
e_tot_min = e_tot
indx_min = int(tmp)
indx_pop_min = indx_pop
if mode == "2D":
poscar = "POSCAR_POP" + str(indx_pop) + "_" + str(indx)
struct = read_vasp(poscar)
cell = struct.get_cell()
z = cell[2][2]
if e_tot < e_tot_min and z > 8. and e_tot > -25.: # z>8. -> 2D, e_tot/at > -25. to avoid not converged results
e_tot_min = e_tot
indx_min = int(tmp)
indx_pop_min = indx_pop
# print(indx_pop_min,indx_min)
if calculator == "VASP":
poscar = "POSCAR_POP" + str(indx_pop_min) + "_" + str(indx_min)
struct = read_vasp(poscar)
write(filename='POSCAR.best', images=struct, format='vasp')
write(filename='POSCAR.best.in',
images=struct,
format='espresso-in')
if calculator == "siesta":
outfile = "siesta.XV." + str(indx_min) + ".POP" + str(indx_pop_min)
struct = xv_to_atoms(outfile)
write(filename='POSCAR.best', images=struct, format='vasp')
write(filename='POSCAR.best.in',
images=struct,
format='espresso-in')
if calculator == "openmx":
# raise ValueError('not yet implemented for openmx case')
outfile = "openmx.dat#." + str(indx_min) + ".POP" + str(
indx_pop_min)
pos, species, cell = read_openmx_hashfile(outfile)
struct = Atoms(species)
struct.set_positions(pos)
struct.set_cell(cell)
write(filename='POSCAR.best', images=struct, format='vasp')
write(filename='POSCAR.best.in',
images=struct,
format='espresso-in')
return e_tot_min
kargs=ma.getPropertyFromPosition(xlabel=r'Time',ylabel=r'EField')
ma.setProperty(ax,**kargs)
#for i, k in enumerate(kpath):
# n = i/nkx
# if n % 2 == 1:
# kpath[i] = 2*n*nkx + nkx - i - 1
ax = axs[0]
kpath = np.arange(exe.shape[1])
from ase.calculators.siesta.import_functions import xv_to_atoms
points = special_points['hexagonal']
points['K1']= [-0.3333, 0.333, 0]
points['K2']= [0.666, 0.333, 0]
kline = ['K2','K1','K2']
xticks, kinfo = dp.findBandPath(xv_to_atoms('siesta.XV'),points,kline,toleAngle=0.001)
kpath = kinfo['uc-index']
x = kinfo['distance']
print x
#print list(kpath+1)
evolvingBands = range(exe.shape[2])
excited = np.abs(exe[1,kpath,:] - exe[0,kpath,:])
norm = 1000.0/np.max(exe[:,kpath,:] - exe[0,kpath,:])
eigenvalue = eigen[0,kpath,:]
#print eigenvalue.shape, excited.shape, x.shape
line = []
scatter = []
def generateStructPNG(atoms=None,
rotation=[0, 0, 0],
camera='perspective',
repeat=[1, 1, 1],
cell=False,
**args):
from ase.calculators.siesta.import_functions import xv_to_atoms
from ase.io import write
if atoms is None:
atoms = xv_to_atoms('siesta.XV')
rot = str(rotation[0]) + 'x,' + str(rotation[1]) + 'y,' + str(
rotation[2]) + 'z'
if cell:
showcell = 2
else:
showcell = 0
kwargs = {
'rotation': rot, # text string with rotation (default='' )
'radii': 1.0, # float, or a list with one float per atom
'colors': None, # List: one (r, g, b) tuple per atom
'show_unit_cell':
showcell, # 0, 1, or 2 to not show, show, and show all of cell
}
kwargs.update({
'run_povray':
True, # Run povray or just write .pov + .ini files
'display':
False, # Display while rendering
'pause':
True, # Pause when done rendering (only if display)
'transparent':
True, # Transparent background
'canvas_width':
None, # Width of canvas in pixels
'canvas_height':
800, # Height of canvas in pixels
'camera_dist':
12000., # Distance from camera to front atom
'image_plane':
0, # Distance from front atom to image plane
'camera_type':
camera, # perspective, ultra_wide_angle, orthographic
'point_lights': [], # [[loc1, color1], [loc2, color2],...]
'area_light': [
(2., 3., 40.), # location
'White', # color
.7,
.7,
3,
3
], # width, height, Nlamps_x, Nlamps_y
'background':
'White', # color
'textures':
None, # Length of atoms list of texture names
'celllinewidth':
0.1, # Radius of the cylinders representing the cell
})
cell = atoms.cell
atoms.center()
atoms = atoms * repeat
for position in atoms.positions:
position -= repeat[0] / 2 * cell[0, :]
position -= repeat[1] / 2 * cell[1, :]
position -= repeat[2] / 2 * cell[2, :]
atoms.cell = cell
write('struct.pov', atoms, **kwargs)
def action(index, folder):
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = E_ks[start:,] - E_ks[2]
atoms = xv_to_atoms('siesta.XV')
return index, folder, timeEn, deltaE, atoms
