for ind_mol in xrange(len(mols)):
mol = mols[ind_mol].group
kink = mols[ind_mol].kinked
klocation = mols[ind_mol].klocation
imgfolder2=paths + '/' + imgfolder + '/diffusion' + str(mol)
try:
os.mkdir(imgfolder2)
except:
pass
# READ IN TIME-DEP CENTER OF MASS OF H**O
inputfile = os.path.join(paths,datafolder,'runninghomoCOMVEL_mol' + str(mol) + '.csv')
lhomo = mf.readinCSV(inputfile, 1)
times[:,ind_mol] =np.asarray([x[0] for x in lhomo], dtype="float") #ALREADY IN ANGSTROM
COMx[:,ind_mol] = np.asarray([x[1] for x in lhomo], dtype="float") #ALREADY IN ANGSTROM
COMy[:,ind_mol] = np.asarray([x[2] for x in lhomo], dtype="float") #ALREADY IN ANGSTROM
COMz[:,ind_mol] = np.asarray([x[3] for x in lhomo], dtype="float") #ALREADY IN ANGSTROM
# READ IN END-to-END VECTOR(S)
endendfile = os.path.join(paths,datafolder, 'runningENDEND_mol' + str(mol) + '.csv')
lee = mf.readinCSV(endendfile, 1)
times[:,ind_mol] =np.asarray([x[0] for x in lee], dtype="float")
BEGeex[:,ind_mol] = np.asarray([x[1] for x in lee], dtype="float")
BEGeey[:,ind_mol] = np.asarray([x[2] for x in lee], dtype="float")
BEGeez[:,ind_mol] = np.asarray([x[3] for x in lee], dtype="float")
ENDeex[:,ind_mol] = np.asarray([x[4] for x in lee], dtype="float")
ENDeey[:,ind_mol] = np.asarray([x[5] for x in lee], dtype="float")
if os.path.exists(os.path.join(paths,frontname)):
os.chdir(os.path.join(paths,frontname))
comxnumrun=[]; comynumrun=[]; comznumrun=[]
print "Frame " + str(i) + " " +str(mol)
com_file='group_' + str(mol) + '_MOL.com'
homocom_file='homoCOMxyz_mol' + str(mol) + '.csv'
int_file='inertiaOUT_mol' + str(mol)+ '.csv'
gyr_file='gyration2OUT_mol' + str(mol)+ '.csv'
uv_file = os.path.join(paths, datafolder, 'runningUNITVECTOR_mol' + str(mol) + '.csv')
# read in files
linert = mf.readinCSV(int_file, 0)
lgyrate = mf.readinCSV(gyr_file, 0)
lcom = mf.readinCSV(com_file, 0)
lhomocom = mf.readinCSV(homocom_file, 1)
luv = mf.readinCSV(uv_file, 1)
COMhx[i-1][ind_mol]=lhomocom[0][0]
COMhy[i-1][ind_mol]=lhomocom[0][1]
COMhz[i-1][ind_mol]=lhomocom[0][2] #ALREADY IN ANGSTROM
INERTprincphx[i-1][ind_mol]=linert[3][0]
INERTprincphy[i-1][ind_mol]=linert[4][1]
INERTprincphz[i-1][ind_mol]=linert[5][2]
GYRATEprincphx[i-1][ind_mol]=lgyrate[3][0]
GYRATEprincphy[i-1][ind_mol]=lgyrate[4][1]
imppos_cc_plus = np.zeros([steps-1,len(mols)], dtype=float)
imppos_ccMAG_plus = np.zeros([len(mols),1], dtype=float)
for ind_mol in xrange(len(mols)):
mol = mols[ind_mol].group
kink = mols[ind_mol].kinked
klocation = mols[ind_mol].klocation
dihval_ccMAG = np.zeros([ steps,dihedrals], dtype=float)
dihval_cc = np.zeros([ steps,dihedrals], dtype=float)
dihval_cce = np.zeros([ steps,1], dtype=float)
dihval = np.zeros([steps, dihedrals], dtype=float)
infile1 = os.path.join(paths, datafolder, 'runningInert_mol' + str(mol)+ '.csv')
linert = mf.readinCSV(infile1, 1)
times[:,ind_mol] = np.asarray([x[0] for x in linert], dtype="float")
Ixx[:,ind_mol] = np.asarray([x[1] for x in linert], dtype="float")
Iyy[:,ind_mol] = np.asarray([x[2] for x in linert], dtype="float")
Izz[:,ind_mol] =np.asarray([x[3] for x in linert], dtype="float")
infile2 = os.path.join(paths, datafolder, 'runningGyrate_mol' + str(mol)+ '.csv')
lg2 = mf.readinCSV(infile2,1)
G2xx[:,ind_mol] =np.asarray([x[1] for x in lg2], dtype="float")
G2yy[:,ind_mol] =np.asarray([x[2] for x in lg2], dtype="float")
G2zz[:,ind_mol] =np.asarray([x[3] for x in lg2], dtype="float")
infile3 = os.path.join(paths, datafolder, 'runninghomoCOMVEL_mol' + str(mol) + '.csv')
lcomh = mf.readinCSV(infile3, 1)
eeRrun_nL2 = np.zeros([3, len(timelinspace)], dtype=float)
eeRrun_n = np.zeros([3, len(timelinspace)], dtype=float)
kinkatom1 = np.zeros([3, len(timelinspace)], dtype=float)
kinkatom2 = np.zeros([3, len(timelinspace)], dtype=float)
kloc = np.zeros([3, len(timelinspace)], dtype=float)
for i in mf.itertools(1,1):
frontname = 'frame_' + str(i) + '_groups'
if os.path.exists(os.path.join(paths, frontname)):
print "Frame " + str(i) + " mol-" + str(mol)
os.chdir(os.path.join(paths,frontname))
com_file = 'group_' + str(mol) + '_MOL.com'
lcom = mf.readinCSV(com_file, 0)
weight= np.asarray([x[0] for x in lcom], dtype="int")
xcoords = np.asarray([x[1] for x in lcom], dtype="float")
ycoords = np.asarray([x[2] for x in lcom], dtype="float")
zcoords =np.asarray([x[3] for x in lcom], dtype="float") #METER IN FILE
locL1end[0, i-1] = xcoords[L1end-1] ; locL1end[1, i-1] = ycoords[L1end-1] ; locL1end[2, i-1] = zcoords[L1end-1]
locL2end[0, i-1] = xcoords[L2end-1] ; locL2end[1, i-1] = ycoords[L2end-1] ; locL2end[2, i-1] = zcoords[L2end-1]
if kink == 1:
kinkatom1[0,i-1] = xcoords[klocation[0]];
kinkatom1[1,i-1] = ycoords[klocation[0]];
kinkatom1[2,i-1] = zcoords[klocation[0]];
kinkatom2[0,i-1] = xcoords[klocation[1]];
paths = os.getcwd()
for ind_mol in xrange(len(mols)):
mol = mols[ind_mol].group
kink = mols[ind_mol].kinked
klocation = mols[ind_mol].klocation
""" regular autocorrelation functions"""
Inertinfile = os.path.join(paths, datafolder, 'acorrInert_mol' + str(mol) + ".csv")
Gyrateinfile = os.path.join(paths, datafolder, 'acorrGyrate_mol' + str(mol) + ".csv")
cominfile = os.path.join(paths, datafolder, 'acorrHOMOCOMVEL_mol' + str(mol) + ".csv")
energiesinfile = os.path.join(paths, datafolder, 'acorrEnergies_mol' + str(mol) + ".csv")
linert = mf.readinCSV(Inertinfile, 1)
times[:,ind_mol] = np.asarray([x[0] for x in linert], dtype="float")
Ixxac[:,ind_mol] = np.asarray([x[1] for x in linert], dtype="float")
Iyyac[:,ind_mol] = np.asarray([x[2] for x in linert], dtype="float")
Izzac[:,ind_mol] = np.asarray([x[3] for x in linert], dtype="float")
lgyrate = mf.readinCSV(Gyrateinfile, 1)
G2xxac[:,ind_mol] = np.asarray([x[1] for x in lgyrate], dtype="float")
G2yyac[:,ind_mol] = np.asarray([x[2] for x in lgyrate], dtype="float")
G2zzac[:,ind_mol] = np.asarray([x[3] for x in lgyrate], dtype="float")
lcom = mf.readinCSV(cominfile, 1)
comxac[:,ind_mol] = np.asarray([x[1] for x in lcom], dtype="float")
comyac[:,ind_mol] = np.asarray([x[2] for x in lcom], dtype="float")
comzac[:,ind_mol] = np.asarray([x[3] for x in lcom], dtype="float")