diff --git a/scripts/angle_distribute.py b/scripts/angle_distribute.py index 1f03398..63537d8 100644 --- a/scripts/angle_distribute.py +++ b/scripts/angle_distribute.py @@ -1,6 +1,6 @@ -#!/usr/bin/python +#!/usr/bin/python -# Script: angle_distribute.py +# Script: angle_distribute.py # Purpose: binned angle distributions by angle type # Syntax: angle_distribute.py datafile nbin theta_min theta_max outfile files ... # datafile = lammps data file @@ -17,15 +17,14 @@ import sys from dump import dump from math import sqrt,acos,atan -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 7: - raise StandardError, \ - "Syntax: angle_distribute.py datafile nbin theta_min theta_max outfile files ..." + raise Exception("Syntax: angle_distribute.py datafile nbin theta_min theta_max outfile files ...") -dt = data(argv[1]) +dt = data(argv[1]) nbins = int(argv[2]) theta_min = float(argv[3]) theta_max = float(argv[4]) @@ -40,19 +39,19 @@ atype = nangles * [0] iatom = nangles * [0] jatom = nangles * [0] katom = nangles * [0] -for i in xrange(nangles): +for i in range(nangles): atype[i] = int(angle[i][1] - 1) iatom[i] = int(angle[i][2] - 1) jatom[i] = int(angle[i][3] - 1) katom[i] = int(angle[i][4] - 1) ntypes = 0 -for i in xrange(nangles): ntypes = max(angle[i][1],ntypes) +for i in range(nangles): ntypes = max(angle[i][1],ntypes) ntypes = int(ntypes) ncount = ntypes * [0] bin = nbins * [0] -for i in xrange(nbins): - bin[i] = ntypes * [0] +for i in range(nbins): + bin[i] = ntypes * [0] # read snapshots one-at-a-time @@ -64,24 +63,24 @@ PI = 4.0*atan(1.0) while 1: time = d.next() if time == -1: break - + box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi) - + xprd = box[3] - box[0] - yprd = box[4] - box[1] + yprd = box[4] - box[1] zprd = box[5] - box[2] - - d.unscale() + + d.unscale() d.sort() x,y,z = d.vecs(time,"x","y","z") - - for i in xrange(nangles): - + + for i in range(nangles): + delx1 = x[iatom[i]] - x[jatom[i]] dely1 = y[iatom[i]] - y[jatom[i]] delz1 = z[iatom[i]] - z[jatom[i]] - + if abs(delx1) > 0.5*xprd: if delx1 < 0.0: delx1 += xprd @@ -97,13 +96,13 @@ while 1: delz1 += zprd else: delz1 -= zprd - + r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1) - + delx2 = x[katom[i]] - x[jatom[i]] dely2 = y[katom[i]] - y[jatom[i]] delz2 = z[katom[i]] - z[jatom[i]] - + if abs(delx2) > 0.5*xprd: if delx2 < 0.0: delx2 += xprd @@ -119,38 +118,38 @@ while 1: delz2 += zprd else: delz2 -= zprd - + r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2) - + c = delx1*delx2 + dely1*dely2 + delz1*delz2 c /= r1*r2 - + if (c > 1.0): c = 1.0 if (c < -1.0): c = -1.0 - + theta = 180.0*acos(c)/PI - + ibin = int(nbins*(theta - theta_min)/(theta_max - theta_min) + 0.5) - if ((ibin >= 0) and (ibin <= nbins-1)): + if ((ibin >= 0) and (ibin <= nbins-1)): bin[ibin][atype[i]] += nbins ncount[atype[i]] += 1 else: - print "Warning: angle outside specified range" - print "angle type:", atype[i]+1 - print "angle number:", i - print time, - -print -print "Printing normalized angle distributions to",outfile - + print("Warning: angle outside specified range") + print("angle type:", atype[i]+1) + print("angle number:", i) + print(time, end=' ') + +print() +print("Printing normalized angle distributions to",outfile) + fp = open(outfile,"w") theta_range = theta_max - theta_min -for i in xrange(nbins): - print >>fp, theta_min + theta_range*float(i)/float(nbins), - for j in xrange(ntypes): +for i in range(nbins): + print(theta_min + theta_range*float(i)/float(nbins), end=' ', file=fp) + for j in range(ntypes): if (ncount[j] > 0): - print >>fp, float(bin[i][j])/float(ncount[j])/theta_range, + print(float(bin[i][j])/float(ncount[j])/theta_range, end=' ', file=fp) else: - print >>fp, 0.0, - print >>fp + print(0.0, end=' ', file=fp) + print(file=fp) fp.close() diff --git a/scripts/block.py b/scripts/block.py index 2576904..a6ed3cd 100644 --- a/scripts/block.py +++ b/scripts/block.py @@ -3,7 +3,7 @@ # Script: block.py # Purpose: thermodynamic block averages from LAMMPS log files # Syntax: block.py nblocks nskip log.1 log.2 ... -# nblocks = number of blocks for block averages +# nblocks = number of blocks for block averages # nskip = skip first nskip samples in the log file(s) # files = series of log files (LAMMPS thermo one style only) # Example: block.py 10 0 log.* @@ -13,12 +13,12 @@ import sys from log import log -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 4: - raise StandardError, "Syntax: block.py nblocks nskip log.1 log.2 ..." + raise Exception("Syntax: block.py nblocks nskip log.1 log.2 ...") nblocks = int(argv[1]) nskip = int(argv[2]) @@ -35,24 +35,24 @@ if "Volume" in l.names: volume = l.get("Volume") else: vflag = 0 -print "Computing %g block averages" % nblocks -print "Skipping first %g samples" % nskip +print("Computing %g block averages" % nblocks) +print("Skipping first %g samples" % nskip) n = len(step) n_per_block = (n-nskip)/nblocks k = nskip temperature_ave = [] e_bond_ave = [] -e_pair_ave = [] +e_pair_ave = [] e_total_ave = [] pressure_ave = [] volume_ave = [] -print -print " Block Samples Temperature E_bond E_pair", \ - " E_total Pressure Volume" +print() +print(" Block Samples Temperature E_bond E_pair", \ + " E_total Pressure Volume") -for i in xrange(nblocks): +for i in range(nblocks): temperature_sum = 0 e_bond_sum = 0 e_pair_sum = 0 @@ -60,7 +60,7 @@ for i in xrange(nblocks): pressure_sum = 0 volume_sum = 0 samples = 0 - for j in xrange(n_per_block): + for j in range(n_per_block): temperature_sum += temperature[k] e_bond_sum += e_bond[k] e_pair_sum += e_pair[k] @@ -75,42 +75,42 @@ for i in xrange(nblocks): e_total_ave.append(e_total_sum/samples) pressure_ave.append(pressure_sum/samples) volume_ave.append(volume_sum/samples) - print " %5i %10i %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ + print(" %5i %10i %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ (i+1, samples, temperature_ave[i], e_bond_ave[i], e_pair_ave[i], \ - e_total_ave[i], pressure_ave[i], volume_ave[i]) + e_total_ave[i], pressure_ave[i], volume_ave[i])) grand_ave_temperature = 0.0 grand_ave_e_bond = 0.0 grand_ave_e_pair = 0.0 grand_ave_e_total = 0.0 grand_ave_pressure = 0.0 -grand_ave_volume = 0.0 +grand_ave_volume = 0.0 stdev_temperature = 0.0 stdev_e_bond = 0.0 stdev_e_pair = 0.0 stdev_e_total = 0.0 stdev_pressure = 0.0 -stdev_volume = 0.0 -for i in xrange(nblocks): +stdev_volume = 0.0 +for i in range(nblocks): grand_ave_temperature += temperature_ave[i] grand_ave_e_bond += e_bond_ave[i] grand_ave_e_pair += e_pair_ave[i] grand_ave_e_total += e_total_ave[i] grand_ave_pressure += pressure_ave[i] - grand_ave_volume += volume_ave[i] + grand_ave_volume += volume_ave[i] grand_ave_temperature /= nblocks grand_ave_e_bond /= nblocks grand_ave_e_pair /= nblocks grand_ave_e_total /= nblocks grand_ave_pressure /= nblocks -grand_ave_volume /= nblocks -for i in xrange(nblocks): +grand_ave_volume /= nblocks +for i in range(nblocks): stdev_temperature += (temperature_ave[i] - grand_ave_temperature)* \ (temperature_ave[i] - grand_ave_temperature) stdev_e_bond += (e_bond_ave[i] - grand_ave_e_bond)* \ (e_bond_ave[i] - grand_ave_e_bond) stdev_e_pair += (e_pair_ave[i] - grand_ave_e_pair)* \ - (e_pair_ave[i] - grand_ave_e_pair) + (e_pair_ave[i] - grand_ave_e_pair) stdev_e_total += (e_total_ave[i] - grand_ave_e_total)* \ (e_total_ave[i] - grand_ave_e_total) stdev_pressure += (pressure_ave[i] - grand_ave_pressure)* \ @@ -123,15 +123,15 @@ stdev_e_bond = sqrt(stdev_e_bond/(nblocks-1)) stdev_e_pair = sqrt(stdev_e_pair/(nblocks-1)) stdev_e_total = sqrt(stdev_e_total/(nblocks-1)) stdev_pressure = sqrt(stdev_pressure/(nblocks-1)) -stdev_volume = sqrt(stdev_volume/(nblocks-1)) +stdev_volume = sqrt(stdev_volume/(nblocks-1)) -print " ====================================================", \ - "===================================" - -print " Ave. %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ +print(" ====================================================", \ + "===================================") + +print(" Ave. %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ (grand_ave_temperature, grand_ave_e_bond, grand_ave_e_pair, \ - grand_ave_e_total, grand_ave_pressure, grand_ave_volume) - -print " Stdev %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ + grand_ave_e_total, grand_ave_pressure, grand_ave_volume)) + +print(" Stdev %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \ (stdev_temperature, stdev_e_bond, stdev_e_pair, \ - stdev_e_total, stdev_pressure, stdev_volume) + stdev_e_total, stdev_pressure, stdev_volume)) diff --git a/scripts/bond_distribute.py b/scripts/bond_distribute.py index a059cf4..020e72a 100644 --- a/scripts/bond_distribute.py +++ b/scripts/bond_distribute.py @@ -17,13 +17,12 @@ import sys from dump import dump from math import sqrt -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 7: - raise StandardError, \ - "Syntax: bond_distribute.py datafile nbin rmin rmax outfile files ..." + raise Exception("Syntax: bond_distribute.py datafile nbin rmin rmax outfile files ...") dt = data(argv[1]) nbins = int(argv[2]) @@ -39,17 +38,17 @@ nbonds = len(bond) btype = nbonds * [0] iatom = nbonds * [0] jatom = nbonds * [0] -for i in xrange(nbonds): +for i in range(nbonds): btype[i] = int(bond[i][1] - 1) iatom[i] = int(bond[i][2] - 1) jatom[i] = int(bond[i][3] - 1) ntypes = 0 -for i in xrange(nbonds): ntypes = max(bond[i][1],ntypes) +for i in range(nbonds): ntypes = max(bond[i][1],ntypes) ntypes = int(ntypes) ncount = ntypes * [0] bin = nbins * [0] -for i in xrange(nbins): +for i in range(nbins): bin[i] = ntypes * [0] # read snapshots one-at-a-time @@ -72,7 +71,7 @@ while 1: d.sort() x,y,z = d.vecs(time,"x","y","z") - for i in xrange(nbonds): + for i in range(nbonds): delx = x[jatom[i]] - x[iatom[i]] dely = y[jatom[i]] - y[iatom[i]] @@ -101,22 +100,22 @@ while 1: bin[ibin][btype[i]] += nbins ncount[btype[i]] += 1 else: - print "Warning: bond distance outside specified range" - print "Bond type:", btype[i]+1 - print "Bond number:", i - print time, + print("Warning: bond distance outside specified range") + print("Bond type:", btype[i]+1) + print("Bond number:", i) + print(time, end=' ') -print -print "Printing bond distance normalized distribution to",outfile +print() +print("Printing bond distance normalized distribution to",outfile) fp = open(outfile,"w") rrange = rmax - rmin -for i in xrange(nbins): - print >>fp, rmin + rrange*float(i)/float(nbins), - for j in xrange(ntypes): +for i in range(nbins): + print(rmin + rrange*float(i)/float(nbins), end=' ', file=fp) + for j in range(ntypes): if (ncount[j] > 0): - print >>fp, float(bin[i][j])/float(ncount[j])/rrange, + print(float(bin[i][j])/float(ncount[j])/rrange, end=' ', file=fp) else: - print >>fp, 0.0, - print >>fp + print(0.0, end=' ', file=fp) + print(file=fp) fp.close() diff --git a/scripts/clogview.py b/scripts/clogview.py index fbf80cb..d37256d 100644 --- a/scripts/clogview.py +++ b/scripts/clogview.py @@ -15,18 +15,18 @@ from clog import clog from plotview import plotview from gnu import gnu from matlab import matlab -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 3: - raise StandardError, "Syntax: clogview.py gnu/matlab files ..." + raise Exception("Syntax: clogview.py gnu/matlab files ...") style = argv[1] files = ' '.join(argv[2:]) c = clog(files) -exec "plot = %s()" % style +exec("plot = %s()" % style) p = plotview(c,plot) p.x = "Time" diff --git a/scripts/cluster.py b/scripts/cluster.py index 80cf2ee..c37dcfe 100644 --- a/scripts/cluster.py +++ b/scripts/cluster.py @@ -18,7 +18,7 @@ import sys from dump import dump from gnu import gnu -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script @@ -62,7 +62,7 @@ def distance(atom1,atom2,box): # main script if len(argv) < 6: - raise StandardError,"cluster.py type1 type2 cutoff nbin dump.1 dump.2 ..." + raise Exception("cluster.py type1 type2 cutoff nbin dump.1 dump.2 ...") type1 = int(argv[1]) type2 = int(argv[2]) @@ -81,20 +81,20 @@ d.aselect.test("$type == %d or $type == %d" % (type1,type2)) cutsq = cutoff*cutoff cluster = nbin*[0] -print "Clustering ..." +print("Clustering ...") flag = 0 while 1: which,time,flag = d.iterator(flag) if flag == -1: break time,box,atoms,bonds,tris = d.viz(which) - print time, + print(time, end=' ') sys.stdout.flush() # loop over all type1 atoms n = len(atoms) - for i in xrange(n): + for i in range(n): itype = atoms[i][1] if itype != type1: continue ncount = 0 @@ -102,7 +102,7 @@ while 1: # loop over all type2 atoms # increment cluster count if distance is within cutoff - for j in xrange(n): + for j in range(n): jtype = atoms[j][1] if jtype != type2 or i == j: continue distsq = distance(atoms[i],atoms[j],box) @@ -113,9 +113,9 @@ while 1: if ncount >= nbin: cluster[nbin-1] += 1 else: cluster[ncount] += 1 -print -print "Cluster size and count:" -for i in range(nbin): print i,cluster[i] +print() +print("Cluster size and count:") +for i in range(nbin): print(i,cluster[i]) # comment out if don't want plot diff --git a/scripts/density.py b/scripts/density.py index a0c0c6e..6babfd3 100644 --- a/scripts/density.py +++ b/scripts/density.py @@ -14,12 +14,12 @@ import sys from dump import dump -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 5: - raise StandardError, "Syntax: density.py x/y/z nbin outfile files ..." + raise Exception("Syntax: density.py x/y/z nbin outfile files ...") direction = argv[1] nbins = int(argv[2]) @@ -41,7 +41,7 @@ while 1: tmp,ntypes = d.minmax("type") ntypes = int(ntypes) bin = nbins * [0] - for i in xrange(nbins): bin[i] = ntypes * [0] + for i in range(nbins): bin[i] = ntypes * [0] first = 0 box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, @@ -52,26 +52,26 @@ while 1: elif direction == "y": type,x = d.vecs(time,"type","y") elif direction == "z": type,x = d.vecs(time,"type","z") - type = map(int,type) + type = list(map(int,type)) natoms = len(type) - for i in xrange(natoms): type[i] -= 1 + for i in range(natoms): type[i] -= 1 - for i in xrange(natoms): + for i in range(natoms): ibin = int(nbins*x[i] + 0.5) if (ibin < 0): ibin += nbins if (ibin > nbins-1): ibin -= nbins bin[ibin][type[i]] += nbins/vol nsnaps += 1 - print time, + print(time, end=' ') -print -print "Printing ", direction, "-directional density distribution in mol/L to",outfile +print() +print("Printing ", direction, "-directional density distribution in mol/L to",outfile) conversion = 1660.53873 # convert from atoms/Angs^3 to mol/L fp = open(outfile,"w") -for i in xrange(nbins): - print >>fp, float(i)/float(nbins), - for j in xrange(ntypes): - print >>fp, conversion*bin[i][j]/nsnaps, - print >>fp +for i in range(nbins): + print(float(i)/float(nbins), end=' ', file=fp) + for j in range(ntypes): + print(conversion*bin[i][j]/nsnaps, end=' ', file=fp) + print(file=fp) fp.close() diff --git a/scripts/density2d.py b/scripts/density2d.py index e87ad31..b0e12f4 100644 --- a/scripts/density2d.py +++ b/scripts/density2d.py @@ -18,12 +18,12 @@ import sys import numpy as np from dump import dump -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 5: - raise StandardError, "Syntax: density.py x/y/z nbin vmin vmax outfile files ..." + raise Exception("Syntax: density.py x/y/z nbin vmin vmax outfile files ...") direction = argv[1] nbins = int(argv[2]) @@ -102,11 +102,11 @@ while 1: zmin = max(zmin,box[0]) vol = dx * dy * float(zmax - zmin) - type = map(int,type) + type = list(map(int,type)) natoms = len(type) - for i in xrange(natoms): type[i] -= 1 + for i in range(natoms): type[i] -= 1 - for i in xrange(natoms): + for i in range(natoms): ibin = int(nbins*x[i]) jbin = int(nbins*y[i]) zloc = float(z[i])*float(dz) @@ -117,10 +117,10 @@ while 1: if (jbin > nbins-1): jbin = nbins - 1 bin[jbin][ibin][type[i]] += nbins*nbins/vol nsnaps += 1 - print time, + print(time, end=' ') -print -print "Printing %s-mapped density distribution for %s-slice [%.2f,%.2f] in mol/L to %s" %(bidirect, direction, zmin, zmax, outfile) +print() +print("Printing %s-mapped density distribution for %s-slice [%.2f,%.2f] in mol/L to %s" %(bidirect, direction, zmin, zmax, outfile)) conversion = 1660.53873 # convert from atoms/Angs^3 to mol/L fp = open(outfile,"w") @@ -129,10 +129,10 @@ fp = open(outfile,"w") # for k in xrange(ntypes): # print >>fp, " %8s " %(k), # print >>fp -for i in xrange(nbins): - for j in xrange(nbins): - print >>fp, " %8.3f %8.3f " %(float(i)/float(nbins)*float(dx)+float(x0), float(j)/float(nbins)*float(dy)+float(y0)), - for k in xrange(ntypes): - print >>fp, " %8.3f " % (conversion*bin[j][i][k]/nsnaps), - print >>fp +for i in range(nbins): + for j in range(nbins): + print(" %8.3f %8.3f " %(float(i)/float(nbins)*float(dx)+float(x0), float(j)/float(nbins)*float(dy)+float(y0)), end=' ', file=fp) + for k in range(ntypes): + print(" %8.3f " % (conversion*bin[j][i][k]/nsnaps), end=' ', file=fp) + print(file=fp) fp.close() diff --git a/scripts/density_area.py b/scripts/density_area.py index e65a7f0..eded219 100644 --- a/scripts/density_area.py +++ b/scripts/density_area.py @@ -16,12 +16,12 @@ import sys from dump import dump -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 5: - raise StandardError, "Syntax: density.py x/y/z nbin outfile files ..." + raise Exception("Syntax: density.py x/y/z nbin outfile files ...") direction = argv[1] nbins = int(argv[2]) @@ -44,7 +44,7 @@ while 1: tmp,ntypes = d.minmax("type") ntypes = int(ntypes) bin = nbins * [0] - for i in xrange(nbins): bin[i] = ntypes * [0] + for i in range(nbins): bin[i] = ntypes * [0] first = 0 box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo, @@ -55,21 +55,21 @@ while 1: elif direction == "y": type,x = d.vecs(time,"type","y") elif direction == "z": type,x = d.vecs(time,"type","z") - type = map(int,type) + type = list(map(int,type)) natoms = len(type) - for i in xrange(natoms): type[i] -= 1 + for i in range(natoms): type[i] -= 1 - for i in xrange(natoms): + for i in range(natoms): ibin = int(nbins*x[i] + 0.5) if (ibin < 0): ibin += nbins if (ibin > nbins-1): ibin -= nbins bin[ibin][type[i]] += nbins/vol nsnaps += 1 - print time, + print(time, end=' ') -print -print "Printing ",direction,"-directional density distribution in mol/L to", \ - outfile +print() +print("Printing ",direction,"-directional density distribution in mol/L to", \ + outfile) conversion = 1660.53873 # convert from atoms/Angs^3 to mol/L # Output as x, density_1, area_1, ... @@ -78,20 +78,20 @@ fp = open(outfile,"w") first = 1 xden = nbins * [0] yden = nbins * [0] -for i in xrange(nbins): yden[i] = ntypes * [0] +for i in range(nbins): yden[i] = ntypes * [0] sum = ntypes * [0] -for i in xrange(nbins): +for i in range(nbins): xden[i] = float(i)/float(nbins) - print >>fp, xden[i], + print(xden[i], end=' ', file=fp) if first: - for j in xrange(ntypes): + for j in range(ntypes): yden[i][j] = conversion*bin[i][j]/nsnaps - print >>fp, yden[i][j], sum[j], + print(yden[i][j], sum[j], end=' ', file=fp) first = 0 else: - for j in xrange(ntypes): + for j in range(ntypes): yden[i][j] = conversion*bin[i][j]/nsnaps sum[j] += 0.5 * (xden[i] - xden[i-1]) * (yden[i][j] + yden[i-1][j]) - print >>fp, yden[i][j], sum[j], - print >>fp + print(yden[i][j], sum[j], end=' ', file=fp) + print(file=fp) fp.close() diff --git a/scripts/distance.py b/scripts/distance.py index 2738847..1848de2 100644 --- a/scripts/distance.py +++ b/scripts/distance.py @@ -12,7 +12,7 @@ from math import sqrt if len(argv) < 3: - raise StandardError,"distance.py maxcut dump.file1 dump.file2 ..." + raise Exception("distance.py maxcut dump.file1 dump.file2 ...") maxcut = float(argv[1]) maxcut_sq = maxcut*maxcut @@ -36,8 +36,8 @@ while 1: yprd = box[4] - box[1] zprd = box[5] - box[2] - for i in xrange(n): - for j in xrange(i+1,n): + for i in range(n): + for j in range(i+1,n): delx = x[j] - x[i] if abs(delx) > 0.5*xprd: @@ -65,11 +65,11 @@ while 1: rsq = delx*delx + dely*dely + delz*delz if rsq < maxcut_sq: - print "time = %d, id[i] = %d, id[j] = %d," \ + print("time = %d, id[i] = %d, id[j] = %d," \ " type[i] = %d, type[j] = %d, distance = %g" % \ - (time, id[i], id[j], type[i], type[j], sqrt(rsq)) + (time, id[i], id[j], type[i], type[j], sqrt(rsq))) d.tselect.none() d.tselect.one(time) - print "timestep = ", time + print("timestep = ", time) d.delete() diff --git a/scripts/dview.py b/scripts/dview.py index 7335847..94fb2de 100644 --- a/scripts/dview.py +++ b/scripts/dview.py @@ -10,7 +10,7 @@ # main script if len(argv) < 2: - raise StandardError, "Syntax: dview.py dump.1 ..." + raise Exception("Syntax: dview.py dump.1 ...") files = ' '.join(argv[1:]) diff --git a/scripts/dview_standalone.py b/scripts/dview_standalone.py index 022f2b8..5ac0fb3 100755 --- a/scripts/dview_standalone.py +++ b/scripts/dview_standalone.py @@ -13,18 +13,18 @@ import sys from dump import dump # w/out Pizza.py these lines need to come before import of gl tool -import Tkinter -tkroot = Tkinter.Tk() +import tkinter +tkroot = tkinter.Tk() tkroot.withdraw() from gl import gl from vcr import vcr -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 2: - raise StandardError, "Syntax: dview.py dump.1 ..." + raise Exception("Syntax: dview.py dump.1 ...") files = ' '.join(argv[1:]) diff --git a/scripts/flux.py b/scripts/flux.py index 1a4ba05..e3f753c 100644 --- a/scripts/flux.py +++ b/scripts/flux.py @@ -14,12 +14,12 @@ import sys from dump import dump -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 5: - raise StandardError, "Syntax: flux.py x/y/z plane outfile files ..." + raise Exception("Syntax: flux.py x/y/z plane outfile files ...") direction = argv[1] scaled_plane = float(argv[2]) @@ -58,7 +58,7 @@ while 1: prd = hi - lo plane = lo + scaled_plane*prd - print time, + print(time, end=' ') sys.stdout.flush() natoms = len(x) @@ -67,7 +67,7 @@ while 1: typeflux = ntypes * [0] - for i in xrange(natoms): + for i in range(natoms): id[i] = int(id[i]) type[i] = int(type[i]) if jconfig == 1: x_initial[id[i]] = x[i] @@ -78,10 +78,10 @@ while 1: crossings = int((plane - x[i])/prd) + 1 typeflux[type[i]] -= crossings - print >>f,time, - for j in xrange(ntypes-1): - print >>f,typeflux[j+1], - print >>f -print + print(time, end=' ', file=f) + for j in range(ntypes-1): + print(typeflux[j+1], end=' ', file=f) + print(file=f) +print() f.close() diff --git a/scripts/iview.py b/scripts/iview.py index 6509f1c..2fce94f 100644 --- a/scripts/iview.py +++ b/scripts/iview.py @@ -11,10 +11,10 @@ import sys from animate import animate -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script # this could be done with one-line alias in shell start-up file -if len(argv) < 2: raise StandardError, "Syntax: iview.py files ..." +if len(argv) < 2: raise Exception("Syntax: iview.py files ...") a = animate(' '.join(argv[1:])) diff --git a/scripts/logview.py b/scripts/logview.py index 79dad87..e48a590 100644 --- a/scripts/logview.py +++ b/scripts/logview.py @@ -15,17 +15,17 @@ from log import log from plotview import plotview from gnu import gnu from matlab import matlab -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 3: - raise StandardError, "Syntax: logview.py gnu/matlab files ..." + raise Exception("Syntax: logview.py gnu/matlab files ...") style = argv[1] files = ' '.join(argv[2:]) lg = log(files) -exec "plot = %s()" % style +exec("plot = %s()" % style) p = plotview(lg,plot) diff --git a/scripts/movie.py b/scripts/movie.py index a38c943..2189ad9 100644 --- a/scripts/movie.py +++ b/scripts/movie.py @@ -15,12 +15,12 @@ import sys from dump import dump from raster import raster from svg import svg -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) < 5: - raise StandardError, "Syntax: movie.py raster/svg theta phi dump.1 ..." + raise Exception("Syntax: movie.py raster/svg theta phi dump.1 ...") style = argv[1] theta = float(argv[2]) @@ -28,6 +28,6 @@ phi = float(argv[3]) files = ' '.join(argv[4:]) d = dump(files) -exec "viz = %s(d)" % style +exec("viz = %s(d)" % style) viz.rotate(theta,phi) viz.all() diff --git a/scripts/plot.py b/scripts/plot.py index 4311149..f101a5d 100644 --- a/scripts/plot.py +++ b/scripts/plot.py @@ -14,17 +14,17 @@ import sys from plotview import plotview from gnu import gnu from matlab import matlab -if not globals().has_key("argv"): argv = sys.argv +if "argv" not in globals(): argv = sys.argv # main script if len(argv) != 3: - raise StandardError, "Syntax: plot.py gnu/matlab file" + raise Exception("Syntax: plot.py gnu/matlab file") style = argv[1] file = argv[2] v = vec(file) -exec "plot = %s()" % style +exec("plot = %s()" % style) p = plotview(v,plot)