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")