def main(argv):
assert len(argv) == 3, "Usage: %s <in.trr> <out.xf.npy>" % argv[0]
t = xdrfile(argv[1])
xf = []
for f in t:
xf.append([f.x.copy(), f.f.copy()])
# convert to Ang, kcal/mol/Ang
xf = array(xf)
xf[:, 0] *= 10.0
xf[:, 1] *= 0.1 / 4.184
save(argv[2], xf)
print("Remember to check for artifacts from periodicity"
" (not corrected here).")
def run(name):
# Define the molecule.
calc, D = mk_calc("sys.py")
trj = xdrfile(name)
#vir = zeros(6)
#N = trj.natoms/M
#dx = zeros((N, 3))
g = trj.__iter__()
frame = g.next()
#trj.seek(0)
print frame.box
K = 128
s = Sfac(SofL(frame.box), array([K, K, K], dtype=int), 4)
s.set_A(ewald_f)
Q = zeros((D, K, K, s.data.ldim), complex128)
C = zeros((D * (D + 1) / 2, K, K, s.data.ldim), complex128)
S = 0
print >> sys.stderr, "Working",
for frame in g:
L = frame.box
wts, cm = calc(frame.x, L)
for i in range(D):
s.sfac(len(cm[i]), wts[i], cm[i].astype(float64))
Q[i] = s.S()
k = 0
for i in range(D):
for j in range(i, D):
C[k] += Q[i] * Q[j].conjugate()
k += 1
S += 1
#s.de1(vir)
#s.de2(N, q, x, dx)
#vir *= Cfac
#dx *= Cfac
#print dx/q[:,newaxis]
#print frame.f - dx
if S % 100 == 0:
print >> sys.stderr, '\b.',
print >> sys.stderr, "\n"
C /= float(S)
save("correl.npy", C)
def __init__(self, inputP ):
# class variable
# self.traj[i, j, k ]: i , ith frame
# j , jth atom
# k , 0 1 2 -- x, y, z
# self.box[i, j] : i, ith frame
# : j, box x, y ,z dimention
# self.timeStep : timeStep between frames
# self.molPair : initial pairs
# self.nFrames : total # of frames in traj
# self.inputP : inputP ; keep it will be convinient
trajFn = inputP['-f']
molFn = inputP['-n']
self.inputP = inputP
# read traj
tmpx = []
tmpbox = []
tmpT1 = -1
tmpT2 = -1
for f in xdrfile.xdrfile(trajFn):
tmpx.append( copy.deepcopy(f.x) )
tmpbox.append( np.diag( copy.deepcopy(f.box) ) )
if tmpT1 == -1 and tmpT2 == -1:
tmpT1 = f.time
elif tmpT1 != -1 and tmpT2 == -1:
tmpT2 = f.time
self.timeStep = tmpT2 - tmpT1
else:
tmpT1 = tmpT2
tmpT2 = f.time
if self.timeStep != tmpT2 - tmpT1 :
print >> sys.stderr, 'Time step changed ! '
sys.exit(1)
if _debug:
if f.time > 20.0 :
break
self.traj = np.array( tmpx )
self.nFrames = np.size(self.traj , 0 )
self.box = np.array( tmpbox )
if _debug:
pass
#print self.box
#print self.traj
# read mol index
# format i ,j start from index 0
self.molPair = []
for i in open(molFn):
tmp1 , tmp2 = map(int , i.split() )
self.molPair.append( (tmp1 -1, tmp2 -1) )
if _debug:
#print self.molPair
print self.timeStep
def __init__(self, inputP ):
# class variable
# self.traj[i, j, k ]: i , ith frame
# j , jth atom
# k , 0 1 2 -- x, y, z
# self.molPair : molPair to calcualte relative diffusion
# self.timeStep : timeStep between frames
# self.skip : skip # of frames
# self.fout : file handler of output file
# self.nFrames : total # of frames in traj
# self.deltaF : [] of delta frames for diffusion
# self.msdAllPair : dictionary stores that msd of all pairs
# if -thread is set , we need to multi threading .
# self.flagThread : if it is set, we do multi thread
# self.flagExitThread : exit flag for all thread when self.queue is empty
# self.queueLock : lock for the Queue
# self.queue : queue for ( i, j ) mol pairs
# self.threads : list of all threads and used for join
# self.nThreads : number of threads
trajFn = inputP['-f']
molFn = inputP['-n']
# read traj
tmpx = []
# tmpbox = []
tmpT1 = -1
tmpT2 = -1
self.msdAllPair = {}
for f in xdrfile.xdrfile(trajFn):
tmpx.append( copy.deepcopy(f.x) )
#tmpbox.append( copy.deepcopy(f.box) )
if tmpT1 == -1 and tmpT2 == -1:
tmpT1 = f.time
elif tmpT1 != -1 and tmpT2 == -1:
tmpT2 = f.time
self.timeStep = tmpT2 - tmpT1
else:
tmpT1 = tmpT2
tmpT2 = f.time
if self.timeStep != tmpT2 - tmpT1 :
print >> sys.stderr, 'Time step changed ! '
sys.exit(1)
if _debug:
if f.time > 80.0 :
break
self.traj = np.array( tmpx )
self.nFrames = np.size(self.traj , 0 )
#self.box = np.array( tmpbox )
self.fout = open( inputP['-o'], 'w' )
if inputP.has_key('-skip'):
self.skip = int( inputP['-skip'] )
else:
self.skip = 1
# nFrames / 10 will only provide 10 data points.
self.deltaF = range(1, self.nFrames/ 10, self.skip )
if _debug:
#print self.box
print self.traj[:, 0, :]
# read mol index
# format i ,j start from index 0
self.molPair = []
for i in open(molFn):
tmp1 , tmp2 = map(int , i.split() )
self.molPair.append( (tmp1 -1, tmp2 -1) )
if _debug:
print self.molPair
print self.timeStep
# part for multi thread
if inputP.has_key('-thread'):
self.flagThread = True
else:
self.flagThread = False
if self.flagThread:
# all the things to set thread environment
self.queueLock = threading.Lock()
self.queue = Queue.Queue()
self.queueLock.acquire()
for i in self.molPair:
self.queue.put( i )
self.queueLock.release()
self.threads = []
self.nThreads = int( inputP['-thread'] )
self.flagExitThread = False
# set symmetry flag
symmFlag = False
if inputP.has_key('-c'):
symmFlag = True
cIdx = int( inputP['-c'] )
frame_c =0
global_time = 0
if type(inputP['-f']) is not list:
inputP['-f'] = [ inputP['-f'] ]
for xtc_f in inputP['-f']:
for f in xdrfile.xdrfile(xtc_f) :
global_time += 1
# print every 100 ps
if time_step > 1:
if global_time % time_step != 0 : continue
if global_time > time_end:
break
if global_time >= time_start :
if global_time % 100 == 0 :
sys.stdout.write("reading frame : %10.3f frames\r" % (global_time) )
def __init__(self, inputP):
# class variable
# self.traj[i, j, k ]: i , ith frame
# j , jth atom
# k , 0 1 2 -- x, y, z
# self.box[i, j] : i, ith frame
# : j, box x, y ,z dimention
# self.timeStep : timeStep between frames
# self.molPair : initial pairs
# self.skip : number of frames to skip in survial time
# self.cutoff : cutoff
# self.nFrames : total # of frames in traj
# self.inputP : inputP ; keep it will be convinient
# self.nsample : number of random start points draw from first half of the data
trajFn = inputP["-f"]
molFn = inputP["-n"]
self.inputP = inputP
# read traj
tmpx = []
tmpbox = []
tmpT1 = -1
tmpT2 = -1
for f in xdrfile.xdrfile(trajFn):
tmpx.append(copy.deepcopy(f.x))
tmpbox.append(np.diag(copy.deepcopy(f.box)))
if tmpT1 == -1 and tmpT2 == -1:
tmpT1 = f.time
elif tmpT1 != -1 and tmpT2 == -1:
tmpT2 = f.time
self.timeStep = tmpT2 - tmpT1
else:
tmpT1 = tmpT2
tmpT2 = f.time
if self.timeStep != tmpT2 - tmpT1:
print >> sys.stderr, "Time step changed ! "
sys.exit(1)
if _debug:
if f.time > 20.0:
break
self.traj = np.array(tmpx)
self.nFrames = np.size(self.traj, 0)
self.box = np.array(tmpbox)
self.nsample = int(inputP["-nsample"])
self.skip = int(inputP["-skip"])
self.cutoff = float(inputP["-cutoff"])
if _debug:
pass
# print self.box
# print self.traj
# read mol index
# format i ,j start from index 0
self.molPair = []
for i in open(molFn):
tmp1, tmp2 = map(int, i.split())
self.molPair.append((tmp1 - 1, tmp2 - 1))
if _debug:
# print self.molPair
print self.timeStep
def __init__(self, inputP ):
# class variable
# self.traj[i, j, k ]: i , ith frame
# j , jth atom
# k , 0 1 2 -- x, y, z
# self.molPair : molPair to calcualte relative diffusion
# self.timeStep : timeStep between frames
# self.skip : skip # of frames
# self.fout : file handler of output file
# self.nFrames : total # of frames in traj
# self.deltaF : [] of delta frames for diffusion
trajFn = inputP['-f']
molFn = inputP['-n']
# read traj
tmpx = []
# tmpbox = []
tmpT1 = -1
tmpT2 = -1
for f in xdrfile.xdrfile(trajFn):
tmpx.append( copy.deepcopy(f.x) )
#tmpbox.append( copy.deepcopy(f.box) )
if tmpT1 == -1 and tmpT2 == -1:
tmpT1 = f.time
elif tmpT1 != -1 and tmpT2 == -1:
tmpT2 = f.time
self.timeStep = tmpT2 - tmpT1
else:
tmpT1 = tmpT2
tmpT2 = f.time
if self.timeStep != tmpT2 - tmpT1 :
print >> sys.stderr, 'Time step changed ! '
sys.exit(1)
if _debug:
if f.time > 80.0 :
break
self.traj = np.array( tmpx )
self.nFrames = np.size(self.traj , 0 )
#self.box = np.array( tmpbox )
self.fout = open( inputP['-o'], 'w' )
if inputP.has_key('-skip'):
self.skip = int( inputP['-skip'] )
else:
self.skip = 1
# nFrames / 10 will only provide 10 data points.
self.deltaF = range(1, self.nFrames/ 10, self.skip )
if _debug:
#print self.box
print self.traj[:, 0, :]
# read mol index
# format i ,j start from index 0
self.molPair = []
for i in open(molFn):
tmp1 , tmp2 = map(int , i.split() )
self.molPair.append( (tmp1 -1, tmp2 -1) )
if _debug:
print self.molPair
print self.timeStep
