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import os
import shutil
import numpy as np
import matplotlib as mpl
import math
mpl.use('Agg')
from matplotlib import pyplot as plt
from optparse import OptionParser
import sys
from copy import deepcopy
class debug(object):
def __init__(self,info='debug'):
self.info=info
def __call__(self,func):
def wrapper(*args,**kwargs):
print('[{info}] Now entering function {function}.....' \
.format(info=self.info,function=getattr(func,"__name__")))
return func(*args,**kwargs)
return wrapper
class Energy_Temp(object):
def __init__(self):
'Read vasp MD energies and temperature.'
self.temp=[]
self.energy=[]
self.energy_extract()
def energy_extract(self):
print('Now reading vasp MD energies and temperature.')
if os.path.exists("OSZICAR"):
oszicar=open("OSZICAR",'r')
for index,line in enumerate(oszicar):
if "E0=" in line:
self.temp.append(float(line.split()[2]))
self.energy.append(float(line.split()[4]))
oszicar.close()
else:
raise IOError('OSZICAR does not exist!')
class XDATCAR(Energy_Temp):
def __init__(self):
'Read lattice information and atomic coordinate.'
super(XDATCAR,self).__init__()
print('Now reading vasp XDATCAR.')
self.lattice=np.zeros((3,3))
self.NPT=False
self.frames=0
self._timestep=1
self.alpha=0.0
self.beta=0.0
self.gamma=0.0
self.current_frame=0
self._lattice1=0.0
self._lattice2=0.0
self._lattice3=0.0
self._lattice=np.zeros(3)
self.format_trans=False
@property
def timestep(self):
return self._timestep
@timestep.setter
def timestep(self,new_time_step):
self._timestep=new_time_step
if os.path.exists("XDATCAR"):
self.XDATCAR=open("XDATCAR",'r')
else:
raise IOError('XDATCAR does not exist!')
title=self.XDATCAR.readline().strip()
for index,line in enumerate(self.XDATCAR):
if "Direct" in line:
self.frames+=1
self.XDATCAR.seek(0)
self.lattice_read()
self.XDATCAR.readline()
for i in range(self.total_atom):
self.XDATCAR.readline()
if "Direct configuration" not in self.XDATCAR.readline():
self.NPT=True
print('Total frames {0}, NpT is {1}'.format(self.frames,self.NPT))
self.XDATCAR.seek(0)
self.lowrange=0;self.uprange=self.frames-1
if self.NPT == False: self.lattice_read()
def step_select(self,selected_step):
'eg. t > 100 and t < 1000'
assert isinstance(selected_step,str),'Selected timestep must be in a "string"'
if 'and' in selected_step:
conditions=selected_step.split("and")
else:
conditions=[selected_step]
for condition in conditions:
try:
if '>=' in condition:
ranges=int(condition.split('>=')[1].strip())
self.lowrange=ranges-1
elif '<=' in condition:
ranges=int(condition.split('<=')[1].strip())
self.uprange=ranges-1
elif '>' in condition:
ranges=int(condition.split('>')[1].strip())
self.lowrange=ranges
elif '<' in condition:
ranges=int(condition.split('<')[1].strip())
self.uprange=ranges-2
else:
print('Selected timestep is invaid!');continue
except ValueError:
print('Selected timestep is invaid!')
sys.exit(0)
if (self.lowrange >= self.frames-1) or (self.uprange < 0):
raise ValueError('Selected timestep is wrong!')
if self.lowrange < 0: self.lowrange= 0
if self.uprange > self.frames-1: self.uprange= self.frames-1
def lattice_read(self):
self.title=self.XDATCAR.readline().rstrip('\r\n').rstrip('\n')
self.scaling_factor=float(self.XDATCAR.readline())
for i in range(3):
self.lattice[i]=np.array([float(j) for j in self.XDATCAR.readline().split()])
self.lattice*=self.scaling_factor
self._lattice1=np.sqrt(np.sum(np.square(self.lattice[0])))
self._lattice2=np.sqrt(np.sum(np.square(self.lattice[1])))
self._lattice3=np.sqrt(np.sum(np.square(self.lattice[2])))
self._lattice[0]=self._lattice1
self._lattice[1]=self._lattice2
self._lattice[2]=self._lattice3
self.alpha=math.acos(np.dot(self.lattice[1],self.lattice[2]) \
/float((self._lattice2*self._lattice3)))/np.pi*180.0
self.beta=math.acos(np.dot(self.lattice[0],self.lattice[2]) \
/float((self._lattice1*self._lattice3)))/np.pi*180.0
self.gamma=math.acos(np.dot(self.lattice[0],self.lattice[1]) \
/float((self._lattice1*self._lattice2)))/np.pi*180.0
self.element_list=[j for j in self.XDATCAR.readline().split()]
try:
self.element_amount=[int(j) for j in self.XDATCAR.readline().split()]
except ValueError:
raise ValueError('VASP 5.x XDATCAR is needed!')
self.total_elements=[]
for i in range(len(self.element_amount)):
self.total_elements.extend([self.element_list[i]]*self.element_amount[i])
self.total_atom=sum(self.element_amount)
self.atomic_position=np.zeros((self.total_atom,3))
def __iter__(self):
return self
def __next__(self):
self.next()
def skiplines_(self):
if self.NPT == True: self.lattice_read()
self.XDATCAR.readline()
for i in range(self.total_atom):
self.XDATCAR.readline()
def next(self):
if self.NPT == True: self.lattice_read()
self.XDATCAR.readline()
for i in range(self.total_atom):
line_tmp=self.XDATCAR.readline()
self.atomic_position[i]=np.array([float(j) for j in line_tmp.split()[0:3]])
self.cartesian_position=np.dot(self.atomic_position,self.lattice)
self.current_frame+=1
return self.cartesian_position
def writepdb(self,pdb_frame):
tobewriten=[]
tobewriten.append("MODEL %r" %(pdb_frame))
tobewriten.append("REMARK Converted from XDATCAR file")
tobewriten.append("REMARK Converted using VASPKIT")
tobewriten.append('CRYST1{0:9.3f}{1:9.3f}{2:9.3f}{3:7.2f}{4:7.2f}{5:7.2f}' .format(self._lattice1,\
self._lattice2,self._lattice3,self.alpha,self.beta,self.gamma))
for i in range(len(self.total_elements)):
tobewriten.append('%4s%7d%4s%5s%6d%4s%8.3f%8.3f%8.3f%6.2f%6.2f%12s' \
%("ATOM",i+1,self.total_elements[i],"MOL",1,' ',self.cartesian_position[i][0],\
self.cartesian_position[i][1],self.cartesian_position[i][2],1.0,0.0,self.total_elements[i]))
tobewriten.append('TER')
tobewriten.append('ENDMDL')
with open('XDATCAR.pdb','a+') as pdbwriter:
tobewriten=[i+'\n' for i in tobewriten]
pdbwriter.writelines(tobewriten)
def unswrapPBC(self,prev_atomic_cartesian):
diff= self.cartesian_position-prev_atomic_cartesian
prev_atomic_cartesian=deepcopy(self.cartesian_position)
xx=np.where(diff[:,0]>(self._lattice1/2),diff[:,0]-self._lattice1\
,np.where(diff[:,0]<-(self._lattice1/2),diff[:,0]+self._lattice1\
,diff[:,0]))
yy=np.where(diff[:,1]>(self._lattice2/2),diff[:,1]-self._lattice2\
,np.where(diff[:,1]<-(self._lattice2/2),diff[:,1]+self._lattice2\
,diff[:,1]))
zz=np.where(diff[:,2]>(self._lattice3/2),diff[:,2]-self._lattice3\
,np.where(diff[:,2]<-(self._lattice3/2),diff[:,2]+self._lattice3\
,diff[:,2]))
xx=xx.reshape(-1,1);yy=yy.reshape(-1,1);zz=zz.reshape(-1,1)
return (prev_atomic_cartesian,np.concatenate([xx,yy,zz],axis=1))
def reset_cartesian(self,real_atomic_cartesian,center_atom):
if center_atom > len(real_atomic_cartesian)-1:
raise SystemError("Selected atom does not exist!")
for i in range(0,len(real_atomic_cartesian)):
for j in range(3):
if (real_atomic_cartesian[i][j]-real_atomic_cartesian[center_atom][j])>self._lattice[j]/2:
real_atomic_cartesian[i][j]-=self._lattice[j]
if (real_atomic_cartesian[i][j]-real_atomic_cartesian[center_atom][j])<-self._lattice[j]/2:
real_atomic_cartesian[i][j]+=self._lattice[j]
return real_atomic_cartesian
def __call__(self,selected_step):
self.step_select(selected_step)
def __str__(self):
return ('Read lattice information and atomic coordinate.')
__repr__=__str__
class plot(object):
'Plot MD temperature and energy profile'
def __init__(self,lwd,font,dpi,figsize,XDATCAR_inst=None):
self.XDATCAR_inst=XDATCAR_inst;self.timestep=self.XDATCAR_inst.timestep
self.time_range=(self.XDATCAR_inst.lowrange,self.XDATCAR_inst.uprange+1)
self.lwd=lwd;self.font=font;self.dpi=dpi;self.figsize=figsize
def plotfigure(self,title='MD temperature and energy profile'):
from matplotlib import pyplot as plt
self.newtemp=self.XDATCAR_inst.temp;self.newenergy=self.XDATCAR_inst.energy
xdata=np.arange(self.time_range[0],self.time_range[1])*self.timestep
axe = plt.subplot(121)
self.newtemp=self.newtemp[self.time_range[0]:self.time_range[1]]
axe.plot(xdata,self.newtemp, \
color='black', lw=self.lwd, linestyle='-', alpha=1)
with open("Temperature.dat",'w') as writer:
writer.write("Time(fs) Temperature(K)\n")
for line in range(len(xdata)):
writer.write("{0:f} {1:f}\n" .format(xdata[line],self.newtemp[line]))
axe.set_xlabel(r'$Time$ (fs)',fontdict=self.font)
axe.set_ylabel(r'$Temperature$ (K)',fontdict=self.font)
axe.set_xlim((self.time_range[0]*self.timestep, self.time_range[1]*self.timestep))
axe.set_title('MD temperature profile')
axe1 = plt.subplot(122)
self.newenergy=self.newenergy[self.time_range[0]:self.time_range[1]]
axe1.plot(xdata,self.newenergy, \
color='black', lw=self.lwd, linestyle='-', alpha=1)
with open("Energy.dat",'w') as writer:
writer.write("Time(fs) Energy(ev)\n")
for line in range(len(xdata)):
writer.write("{0:f} {1:f}\n" .format(xdata[line],self.newenergy[line]))
axe1.set_xlabel(r'$Time$ (fs)',fontdict=self.font)
axe1.set_ylabel(r'$Energy$ (ev)',fontdict=self.font)
axe1.set_xlim((self.time_range[0]*self.timestep, self.time_range[1]*self.timestep))
axe1.set_title('MD energy profile')
fig = plt.gcf()
fig.set_size_inches(self.figsize)
plt.tight_layout()
plt.savefig('ENERGY.png',bbox_inches='tight',pad_inches=0.1,dpi=self.dpi)
if __name__ == "__main__":
parser = OptionParser()
parser.add_option("-b", "--begin",
dest="begin", default=1,
help="frames begin")
parser.add_option("-e", "--end",
dest="end", default='false',
help="frames end")
parser.add_option("-t", "--timestep",
dest="timestep", default=1.0,
help="timestep per frame")
parser.add_option("-p", "--pdb",
action="store_true", dest="format_trans", default=False,
help="choose whether to convert XDATCAR to PDB!")
parser.add_option("--pbc",
action="store_true", dest="periodic", default=False,
help="choose whether to swrap PBC images!")
parser.add_option("-i", "--index",
dest="index", default=-1,
help="choose which atom to center whole molecule!")
parser.add_option("--interval",
dest="interval", default=1,
help="extract frames interval!")
(options,args) = parser.parse_args()
try:
float(options.timestep)
int(options.index)
_interval=int(options.interval)
int(options.begin)
if options.end != 'false': int(options.end)
except:
raise ValueError('wrong arguments')
XDATCAR_inst=XDATCAR()
XDATCAR_iter=iter(XDATCAR_inst)
if options.format_trans:
XDATCAR_inst.format_trans=True
if os.path.exists("XDATCAR.pdb"):
shutil.copyfile("XDATCAR.pdb","XDATCAR-bak.pdb")
os.remove("XDATCAR.pdb")
else:
XDATCAR_inst.format_trans=False
XDATCAR_inst.timestep=float(options.timestep)
if options.end == 'false':
XDATCAR_inst('t>= %r' %(int(options.begin)))
else:
XDATCAR_inst('t>= %r and t <= %r' %(int(options.begin),int(options.end)))
if _interval >(XDATCAR_inst.uprange-XDATCAR_inst.lowrange):
raise SystemError('Trajectory interval exceed selected time range!')
elif _interval<=1:
_interval=1
count=0
current_pdb=1
for i in range(XDATCAR_inst.uprange+1):
if (i>=XDATCAR_inst.lowrange):
cartesian_position=XDATCAR_iter.next()
if count % _interval == 0:
if options.format_trans == True:
if options.periodic == True:
if i == XDATCAR_inst.lowrange:
real_atomic_cartesian=deepcopy(cartesian_position)
if int(options.index) != -1:
real_atomic_cartesian=XDATCAR_inst.reset_cartesian(real_atomic_cartesian,int(options.index)-1)
XDATCAR_inst.cartesian_position=real_atomic_cartesian
prev_atomic_cartesian=deepcopy(cartesian_position)
else:
prev_atomic_cartesian,diffs=XDATCAR_inst.unswrapPBC(prev_atomic_cartesian)
real_atomic_cartesian+=diffs
XDATCAR_inst.cartesian_position=real_atomic_cartesian
XDATCAR_inst.writepdb(current_pdb)
current_pdb+=1
count+=1
else:
XDATCAR_iter.skiplines_()
newtemp=XDATCAR_inst.temp
newenergy=XDATCAR_inst.energy
print('Finish reading XDATCAR.')
timestep=XDATCAR_inst.timestep
print('Selected time-range:{0}~{1}fs'.format((XDATCAR_inst.lowrange)*timestep,\
(XDATCAR_inst.uprange)*timestep))
XDATCAR_inst.XDATCAR.close()
print('Timestep for new PDB trajectory is :{0}fs'.format(timestep*_interval))
lwd = 0.2
dpi=300
figsize=(5,4)
font = {'family' : 'arial',
'color' : 'black',
'weight' : 'normal',
'size' : 13.0,
}
plots=plot(lwd,font,dpi,figsize,XDATCAR_inst)
plots.plotfigure()
|
