From 24bf97204bbf7f71a2a8659e547043742addea81 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 14 Aug 2015 14:56:57 +0000 Subject: [PATCH 1/4] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13881 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- tools/python/pizza/dump.py | 414 +++++++++++++++++++++++-------------- tools/python/pizza/gnu.py | 2 +- tools/python/pizza/log.py | 10 +- 3 files changed, 262 insertions(+), 164 deletions(-) diff --git a/tools/python/pizza/dump.py b/tools/python/pizza/dump.py index 9f59f27933..3b7e7c46c7 100644 --- a/tools/python/pizza/dump.py +++ b/tools/python/pizza/dump.py @@ -17,8 +17,8 @@ d = dump("dump.*") wildcard expands to multiple files d = dump("dump.*",0) two args = store filenames, but don't read incomplete and duplicate snapshots are deleted - if atoms have 5 or 8 columns, assign id,type,x,y,z (ix,iy,iz) atoms will be unscaled if stored in files as scaled + self-describing column names assigned time = d.next() read next snapshot from dump files @@ -28,7 +28,7 @@ time = d.next() read next snapshot from dump files return -1 if no snapshots left or last snapshot is incomplete no column name assignment or unscaling is performed -d.map(1,"id",3,"x") assign names to atom columns (1-N) +d.map(1,"id",3,"x") assign names to columns (1-N) not needed if dump file is self-describing @@ -61,7 +61,7 @@ d.write("file",head,app) write selected steps/atoms to dump file d.scatter("tmp") write selected steps/atoms to multiple files write() can be specified with 2 additional flags - headd = 0/1 for no/yes snapshot header, app = 0/1 for write vs append + head = 0/1 for no/yes snapshot header, app = 0/1 for write vs append scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc d.scale() scale x,y,z to 0-1 for all timesteps @@ -115,10 +115,9 @@ fx,fy,... = d.vecs(1000,"fx","fy",...) return vector(s) for timestep N vecs() returns vectors with one value for each selected atom in the timestep index,time,flag = d.iterator(0/1) loop over dump snapshots -time,box,atoms,bonds,tris = d.viz(index) return list of viz objects +time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects d.atype = "color" set column returned as "type" by viz -d.extra("dump.bond") read bond list from dump file -d.extra(data) extract bond/tri/line list from data +d.extra(obj) extract bond/tri/line info from obj iterator() loops over selected timesteps iterator() called with arg = 0 first time, with arg = 1 on subsequent calls @@ -126,17 +125,21 @@ d.extra(data) extract bond/tri/line list from data time = timestep value flag = -1 when iteration is done, 1 otherwise viz() returns info for selected atoms for specified timestep index + can also call as viz(time,1) and will find index of preceding snapshot time = timestep value - box = [xlo,ylo,zlo,xhi,yhi,zhi] + box = \[xlo,ylo,zlo,xhi,yhi,zhi\] atoms = id,type,x,y,z for each atom as 2d array bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array - if bonds() was used to define bonds, else empty list + if extra() used to define bonds, else NULL tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3,nx,ny,nz for each tri as 2d array - if extra() was used to define tris, else empty list + if extra() used to define tris, else NULL lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array - if extra() was used to define lines, else empty list + if extra() used to define lines, else NULL atype is column name viz() will return as atom type (def = "type") - extra() stores list of bonds/tris/lines to return each time viz() is called + extra() extracts bonds/tris/lines from obj each time viz() is called + obj can be data object for bonds, cdata object for tris and lines, + bdump object for bonds, tdump object for tris, ldump object for lines. + mdump object for tris """ # History @@ -153,6 +156,7 @@ d.extra(data) extract bond/tri/line list from data # increment = 1 if reading snapshots one-at-a-time # nextfile = which file to read from via next() # eof = ptr into current file for where to read via next() +# scale_original = 0/1/-1 if coords were read in as unscaled/scaled/unknown # nsnaps = # of snapshots # nselect = # of selected snapshots # snaps = list of snapshots @@ -161,20 +165,22 @@ d.extra(data) extract bond/tri/line list from data # tselect = class for time selection # aselect = class for atom selection # atype = name of vector used as atom type by viz extract -# bondflag = 0 if no bonds, 1 if they are defined statically -# bondlist = static list of bonds to viz() return for all snapshots -# only a list of atom pairs, coords have to be created for each snapshot +# bondflag = 0 if no bonds, 1 if they are defined statically, 2 if dynamic +# bondlist = static list of bonds to return w/ viz() for all snapshots # triflag = 0 if no tris, 1 if they are defined statically, 2 if dynamic -# trilist = static list of tris to return via viz() for all snapshots -# lineflag = 0 if no lines, 1 if they are defined statically -# linelist = static list of lines to return via viz() for all snapshots +# trilist = static list of tris to return w/ viz() for all snapshots +# lineflag = 0 if no lines, 1 if they are defined statically, 2 if dynamic +# linelist = static list of lines to return w/ viz() for all snapshots +# objextra = object to get bonds,tris,lines from dynamically # Snap = one snapshot # time = time stamp # tselect = 0/1 if this snapshot selected # natoms = # of atoms +# boxstr = format string after BOX BOUNDS, if it exists +# triclinic = 0/1 for orthogonal/triclinic based on BOX BOUNDS fields # nselect = # of selected atoms in this snapshot # aselect[i] = 0/1 for each atom -# xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float) +# xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz = box bounds (float) # atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1 # Imports and external programs @@ -184,11 +190,11 @@ from os import popen from math import * # any function could be used by set() try: - import numpy as np - oldnumeric = False + import numpy as np + oldnumeric = False except: - import Numeric as np - oldnumeric = True + import Numeric as np + oldnumeric = True try: from DEFAULTS import PIZZA_GUNZIP except: PIZZA_GUNZIP = "gunzip" @@ -210,9 +216,9 @@ class dump: self.bondlist = [] self.triflag = 0 self.trilist = [] - self.triobj = 0 self.lineflag = 0 self.linelist = [] + self.objextra = None # flist = list of all dump file names @@ -263,19 +269,9 @@ class dump: self.tselect.all() - # set default names for atom columns if file wasn't self-describing + # print column assignments - if len(self.snaps) == 0: - print "no column assignments made" - elif len(self.names): - print "assigned columns:",self.names2str() - elif self.snaps[0].atoms == None: - print "no column assignments made" - elif len(self.snaps[0].atoms[0]) == 5: - self.map(1,"id",2,"type",3,"x",4,"y",5,"z") - print "assigned columns:",self.names2str() - elif len(self.snaps[0].atoms[0]) == 8: - self.map(1,"id",2,"type",3,"x",4,"y",5,"z",6,"ix",7,"iy",8,"iz") + if len(self.names): print "assigned columns:",self.names2str() else: print "no column assignments made" @@ -285,10 +281,11 @@ class dump: if (not self.names.has_key("x")) or \ (not self.names.has_key("y")) or \ (not self.names.has_key("z")): - print "no unscaling could be performed" + print "dump scaling status is unknown" elif self.nsnaps > 0: - if self.scaled(self.nsnaps-1): self.unscale() - else: print "dump is already unscaled" + if self.scale_original == 1: self.unscale() + elif self.scale_original == 0: print "dump is already unscaled" + else: print "dump scaling status is unknown" # -------------------------------------------------------------------- # read next snapshot from list of files @@ -333,8 +330,10 @@ class dump: # -------------------------------------------------------------------- # read a single snapshot from file f # return snapshot or 0 if failed - # assign column names if not already done and file is self-describing - # convert xs,xu to x + # for first snapshot only: + # assign column names (file must be self-describing) + # set scale_original to 0/1/-1 for unscaled/scaled/unknown + # convert xs,xu to x in names def read_snapshot(self,f): try: @@ -347,26 +346,62 @@ class dump: snap.aselect = np.zeros(snap.natoms) item = f.readline() + words = item.split("BOUNDS ") + if len(words) == 1: snap.boxstr = "" + else: snap.boxstr = words[1].strip() + if "xy" in snap.boxstr: snap.triclinic = 1 + else: snap.triclinic = 0 + words = f.readline().split() - snap.xlo,snap.xhi = float(words[0]),float(words[1]) - words = f.readline().split() - snap.ylo,snap.yhi = float(words[0]),float(words[1]) - words = f.readline().split() - snap.zlo,snap.zhi = float(words[0]),float(words[1]) + if len(words) == 2: + snap.xlo,snap.xhi,snap.xy = float(words[0]),float(words[1]),0.0 + else: + snap.xlo,snap.xhi,snap.xy = \ + float(words[0]),float(words[1]),float(words[2]) + words = f.readline().split() + if len(words) == 2: + snap.ylo,snap.yhi,snap.xz = float(words[0]),float(words[1]),0.0 + else: + snap.ylo,snap.yhi,snap.xz = \ + float(words[0]),float(words[1]),float(words[2]) + + words = f.readline().split() + if len(words) == 2: + snap.zlo,snap.zhi,snap.yz = float(words[0]),float(words[1]),0.0 + else: + snap.zlo,snap.zhi,snap.yz = \ + float(words[0]),float(words[1]),float(words[2]) + item = f.readline() if len(self.names) == 0: + self.scale_original = -1 + xflag = yflag = zflag = -1 words = item.split()[2:] if len(words): for i in range(len(words)): - if words[i] == "xs" or words[i] == "xu": + if words[i] == "x" or words[i] == "xu": + xflag = 0 self.names["x"] = i - elif words[i] == "ys" or words[i] == "yu": + elif words[i] == "xs" or words[i] == "xsu": + xflag = 1 + self.names["x"] = i + elif words[i] == "y" or words[i] == "yu": + yflag = 0 self.names["y"] = i - elif words[i] == "zs" or words[i] == "zu": + elif words[i] == "ys" or words[i] == "ysu": + yflag = 1 + self.names["y"] = i + elif words[i] == "z" or words[i] == "zu": + zflag = 0 + self.names["z"] = i + elif words[i] == "zs" or words[i] == "zsu": + zflag = 1 self.names["z"] = i else: self.names[words[i]] = i - + if xflag == 0 and yflag == 0 and zflag == 0: self.scale_original = 0 + if xflag == 1 and yflag == 1 and zflag == 1: self.scale_original = 1 + if snap.natoms: words = f.readline().split() ncol = len(words) @@ -387,27 +422,6 @@ class dump: except: return 0 - # -------------------------------------------------------------------- - # decide if snapshot i is scaled/unscaled from coords of first and last atom - - def scaled(self,i): - ix = self.names["x"] - iy = self.names["y"] - iz = self.names["z"] - natoms = self.snaps[i].natoms - if natoms == 0: return 0 - x1 = self.snaps[i].atoms[0][ix] - y1 = self.snaps[i].atoms[0][iy] - z1 = self.snaps[i].atoms[0][iz] - x2 = self.snaps[i].atoms[natoms-1][ix] - y2 = self.snaps[i].atoms[natoms-1][iy] - z2 = self.snaps[i].atoms[natoms-1][iz] - if x1 >= -0.1 and x1 <= 1.1 and y1 >= -0.1 and y1 <= 1.1 and \ - z1 >= -0.1 and z1 <= 1.1 and x2 >= -0.1 and x2 <= 1.1 and \ - y2 >= -0.1 and y2 <= 1.1 and z2 >= -0.1 and z2 <= 1.1: - return 1 - else: return 0 - # -------------------------------------------------------------------- # map atom column names @@ -418,9 +432,8 @@ class dump: j = i + 1 self.names[pairs[j]] = pairs[i]-1 - # delete unselected snapshots - # -------------------------------------------------------------------- + # delete unselected snapshots def delete(self): ndel = i = 0 @@ -435,6 +448,7 @@ class dump: # -------------------------------------------------------------------- # scale coords to 0-1 for all snapshots or just one + # use 6 params as h-matrix to treat orthongonal or triclinic boxes def scale(self,*list): if len(list) == 0: @@ -453,17 +467,52 @@ class dump: # -------------------------------------------------------------------- def scale_one(self,snap,x,y,z): - if snap.atoms == None: return - xprdinv = 1.0 / (snap.xhi - snap.xlo) - yprdinv = 1.0 / (snap.yhi - snap.ylo) - zprdinv = 1.0 / (snap.zhi - snap.zlo) - atoms = snap.atoms - atoms[:,x] = (atoms[:,x] - snap.xlo) * xprdinv - atoms[:,y] = (atoms[:,y] - snap.ylo) * yprdinv - atoms[:,z] = (atoms[:,z] - snap.zlo) * zprdinv - + if snap.xy == 0.0 and snap.xz == 0.0 and snap.yz == 0.0: + xprdinv = 1.0 / (snap.xhi - snap.xlo) + yprdinv = 1.0 / (snap.yhi - snap.ylo) + zprdinv = 1.0 / (snap.zhi - snap.zlo) + atoms = snap.atoms + if atoms != None: + atoms[:,x] = (atoms[:,x] - snap.xlo) * xprdinv + atoms[:,y] = (atoms[:,y] - snap.ylo) * yprdinv + atoms[:,z] = (atoms[:,z] - snap.zlo) * zprdinv + else: + xlo_bound = snap.xlo; xhi_bound = snap.xhi + ylo_bound = snap.ylo; yhi_bound = snap.yhi + zlo_bound = snap.zlo; zhi_bound = snap.zhi + xy = snap.xy + xz = snap.xz + yz = snap.yz + xlo = xlo_bound - min((0.0,xy,xz,xy+xz)) + xhi = xhi_bound - max((0.0,xy,xz,xy+xz)) + ylo = ylo_bound - min((0.0,yz)) + yhi = yhi_bound - max((0.0,yz)) + zlo = zlo_bound + zhi = zhi_bound + h0 = xhi - xlo + h1 = yhi - ylo + h2 = zhi - zlo + h3 = yz + h4 = xz + h5 = xy + h0inv = 1.0 / h0 + h1inv = 1.0 / h1 + h2inv = 1.0 / h2 + h3inv = yz / (h1*h2) + h4inv = (h3*h5 - h1*h4) / (h0*h1*h2) + h5inv = xy / (h0*h1) + atoms = snap.atoms + if atoms != None: + atoms[:,x] = (atoms[:,x] - snap.xlo)*h0inv + \ + (atoms[:,y] - snap.ylo)*h5inv + \ + (atoms[:,z] - snap.zlo)*h4inv + atoms[:,y] = (atoms[:,y] - snap.ylo)*h1inv + \ + (atoms[:,z] - snap.zlo)*h3inv + atoms[:,z] = (atoms[:,z] - snap.zlo)*h2inv + # -------------------------------------------------------------------- # unscale coords from 0-1 to box size for all snapshots or just one + # use 6 params as h-matrix to treat orthongonal or triclinic boxes def unscale(self,*list): if len(list) == 0: @@ -482,15 +531,40 @@ class dump: # -------------------------------------------------------------------- def unscale_one(self,snap,x,y,z): - if snap.atoms == None: return - xprd = snap.xhi - snap.xlo - yprd = snap.yhi - snap.ylo - zprd = snap.zhi - snap.zlo - atoms = snap.atoms - atoms[:,x] = snap.xlo + atoms[:,x]*xprd - atoms[:,y] = snap.ylo + atoms[:,y]*yprd - atoms[:,z] = snap.zlo + atoms[:,z]*zprd - + if snap.xy == 0.0 and snap.xz == 0.0 and snap.yz == 0.0: + xprd = snap.xhi - snap.xlo + yprd = snap.yhi - snap.ylo + zprd = snap.zhi - snap.zlo + atoms = snap.atoms + if atoms != None: + atoms[:,x] = snap.xlo + atoms[:,x]*xprd + atoms[:,y] = snap.ylo + atoms[:,y]*yprd + atoms[:,z] = snap.zlo + atoms[:,z]*zprd + else: + xlo_bound = snap.xlo; xhi_bound = snap.xhi + ylo_bound = snap.ylo; yhi_bound = snap.yhi + zlo_bound = snap.zlo; zhi_bound = snap.zhi + xy = snap.xy + xz = snap.xz + yz = snap.yz + xlo = xlo_bound - min((0.0,xy,xz,xy+xz)) + xhi = xhi_bound - max((0.0,xy,xz,xy+xz)) + ylo = ylo_bound - min((0.0,yz)) + yhi = yhi_bound - max((0.0,yz)) + zlo = zlo_bound + zhi = zhi_bound + h0 = xhi - xlo + h1 = yhi - ylo + h2 = zhi - zlo + h3 = yz + h4 = xz + h5 = xy + atoms = snap.atoms + if atoms != None: + atoms[:,x] = snap.xlo + atoms[:,x]*h0 + atoms[:,y]*h5 + atoms[:,z]*h4 + atoms[:,y] = snap.ylo + atoms[:,y]*h1 + atoms[:,z]*h3 + atoms[:,z] = snap.zlo + atoms[:,z]*h2 + # -------------------------------------------------------------------- # wrap coords from outside box to inside @@ -537,7 +611,8 @@ class dump: # -------------------------------------------------------------------- # wrap coords to same image as atom ID stored in "other" column - + # if dynamic extra lines or triangles defined, owrap them as well + def owrap(self,other): print "Wrapping to other ..." @@ -549,7 +624,7 @@ class dump: iy = self.names["iy"] iz = self.names["iz"] iother = self.names[other] - + for snap in self.snaps: xprd = snap.xhi - snap.xlo yprd = snap.yhi - snap.ylo @@ -563,14 +638,17 @@ class dump: atoms[i][x] += (atoms[i][ix]-atoms[j][ix])*xprd atoms[i][y] += (atoms[i][iy]-atoms[j][iy])*yprd atoms[i][z] += (atoms[i][iz]-atoms[j][iz])*zprd - + # should bonds also be owrapped ? + if self.lineflag == 2 or self.triflag == 2: + self.objextra.owrap(snap.time,xprd,yprd,zprd,ids,atoms,iother,ix,iy,iz) + # -------------------------------------------------------------------- # convert column names assignment to a string, in column order def names2str(self): - ncol = len(self.snaps[0].atoms[0]) pairs = self.names.items() values = self.names.values() + ncol = len(pairs) str = "" for i in xrange(ncol): if i in values: str += pairs[values.index(i)][0] + ' ' @@ -614,6 +692,12 @@ class dump: if len(self.snaps): namestr = self.names2str() if not append: f = open(file,"w") else: f = open(file,"a") + + if "id" in self.names: id = self.names["id"] + else: id = -1 + if "type" in self.names: type = self.names["type"] + else: type = -1 + for snap in self.snaps: if not snap.tselect: continue print snap.time, @@ -624,10 +708,16 @@ class dump: print >>f,snap.time print >>f,"ITEM: NUMBER OF ATOMS" print >>f,snap.nselect - print >>f,"ITEM: BOX BOUNDS" - print >>f,snap.xlo,snap.xhi - print >>f,snap.ylo,snap.yhi - print >>f,snap.zlo,snap.zhi + if snap.boxstr: print >>f,"ITEM: BOX BOUNDS",snap.boxstr + else: print >>f,"ITEM: BOX BOUNDS" + if snap.triclinic: + print >>f,snap.xlo,snap.xhi,snap.xy + print >>f,snap.ylo,snap.yhi,snap.xz + print >>f,snap.zlo,snap.zhi,snap.yz + else: + print >>f,snap.xlo,snap.xhi + print >>f,snap.ylo,snap.yhi + print >>f,snap.zlo,snap.zhi print >>f,"ITEM: ATOMS",namestr atoms = snap.atoms @@ -636,7 +726,7 @@ class dump: if not snap.aselect[i]: continue line = "" for j in xrange(nvalues): - if (j < 2): + if j == id or j == type: line += str(int(atoms[i][j])) + " " else: line += str(atoms[i][j]) + " " @@ -660,10 +750,16 @@ class dump: print >>f,snap.time print >>f,"ITEM: NUMBER OF ATOMS" print >>f,snap.nselect - print >>f,"ITEM: BOX BOUNDS" - print >>f,snap.xlo,snap.xhi - print >>f,snap.ylo,snap.yhi - print >>f,snap.zlo,snap.zhi + if snap.boxstr: print >>f,"ITEM: BOX BOUNDS",snap.boxstr + else: print >>f,"ITEM: BOX BOUNDS" + if snap.triclinic: + print >>f,snap.xlo,snap.xhi,snap.xy + print >>f,snap.ylo,snap.yhi,snap.xz + print >>f,snap.zlo,snap.zhi,snap.yz + else: + print >>f,snap.xlo,snap.xhi + print >>f,snap.ylo,snap.yhi + print >>f,snap.zlo,snap.zhi print >>f,"ITEM: ATOMS",namestr atoms = snap.atoms @@ -897,9 +993,20 @@ class dump: # -------------------------------------------------------------------- # return list of atoms to viz for snapshot isnap + # if called with flag, then index is timestep, so convert to snapshot index # augment with bonds, tris, lines if extra() was invoked - def viz(self,isnap): + def viz(self,index,flag=0): + if not flag: isnap = index + else: + times = self.time() + n = len(times) + i = 0 + while i < n: + if times[i] > index: break + i += 1 + isnap = i - 1 + snap = self.snaps[isnap] time = snap.time @@ -919,18 +1026,22 @@ class dump: atom = snap.atoms[i] atoms.append([atom[id],atom[type],atom[x],atom[y],atom[z]]) - # create list of current bond coords from static bondlist + # create list of bonds from static or dynamic bond list + # then generate bond coords from bondlist # alist = dictionary of atom IDs for atoms list # lookup bond atom IDs in alist and grab their coords # try is used since some atoms may be unselected - # any bond with unselected atom is not returned to viz caller + # any bond with unselected atom is not added to bonds # need Numeric/Numpy mode here bonds = [] if self.bondflag: + if self.bondflag == 1: bondlist = self.bondlist + elif self.bondflag == 2: + tmp1,tmp2,tmp3,bondlist,tmp4,tmp5 = self.objextra.viz(time,1) alist = {} for i in xrange(len(atoms)): alist[int(atoms[i][0])] = i - for bond in self.bondlist: + for bond in bondlist: try: i = alist[bond[2]] j = alist[bond[3]] @@ -940,15 +1051,23 @@ class dump: atom2[2],atom2[3],atom2[4],atom1[1],atom2[1]]) except: continue + # create list of tris from static or dynamic tri list + # if dynamic, could eliminate tris for unselected atoms + tris = [] if self.triflag: if self.triflag == 1: tris = self.trilist elif self.triflag == 2: - timetmp,boxtmp,atomstmp,bondstmp, \ - tris,linestmp = self.triobj.viz(time,1) - + tmp1,tmp2,tmp3,tmp4,tris,tmp5 = self.objextra.viz(time,1) + + # create list of lines from static or dynamic tri list + # if dynamic, could eliminate lines for unselected atoms + lines = [] - if self.lineflag: lines = self.linelist + if self.lineflag: + if self.lineflag == 1: lines = self.linelist + elif self.lineflag == 2: + tmp1,tmp2,tmp3,tmp4,tmp5,lines = self.objextra.viz(time,1) return time,box,atoms,bonds,tris,lines @@ -991,49 +1110,14 @@ class dump: # -------------------------------------------------------------------- # grab bonds/tris/lines from another object + # if static, grab once, else store obj to grab dynamically def extra(self,arg): - # read bonds from bond dump file + # data object, grab bonds statically - if type(arg) is types.StringType: - try: - f = open(arg,'r') - - item = f.readline() - time = int(f.readline()) - item = f.readline() - nbonds = int(f.readline()) - item = f.readline() - if not re.search("BONDS",item): - raise StandardError, "could not read bonds from dump file" - - words = f.readline().split() - ncol = len(words) - for i in xrange(1,nbonds): - words += f.readline().split() - f.close() - - # convert values to int and absolute value since can be negative types - - if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int) - else: bondlist = np.zeros((nbonds,4),np.int) - ints = [abs(int(value)) for value in words] - start = 0 - stop = 4 - for i in xrange(nbonds): - bondlist[i] = ints[start:stop] - start += ncol - stop += ncol - if bondlist: - self.bondflag = 1 - self.bondlist = bondlist - except: - raise StandardError,"could not read from bond dump file" - - # request bonds from data object - - elif type(arg) is types.InstanceType and ".data" in str(arg.__class__): + if type(arg) is types.InstanceType and ".data" in str(arg.__class__): + self.bondflag = 0 try: bondlist = [] bondlines = arg.sections["Bonds"] @@ -1047,9 +1131,10 @@ class dump: except: raise StandardError,"could not extract bonds from data object" - # request tris/lines from cdata object + # cdata object, grab tris and lines statically elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__): + self.triflag = self.lineflag = 0 try: tmp,tmp,tmp,tmp,tris,lines = arg.viz(0) if tris: @@ -1061,14 +1146,29 @@ class dump: except: raise StandardError,"could not extract tris/lines from cdata object" - # request tris from mdump object + # mdump object, grab tris dynamically elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__): - try: - self.triflag = 2 - self.triobj = arg - except: - raise StandardError,"could not extract tris from mdump object" + self.triflag = 2 + self.objextra = arg + + # bdump object, grab bonds dynamically + + elif type(arg) is types.InstanceType and ".bdump" in str(arg.__class__): + self.bondflag = 2 + self.objextra = arg + + # ldump object, grab lines dynamically + + elif type(arg) is types.InstanceType and ".ldump" in str(arg.__class__): + self.lineflag = 2 + self.objextra = arg + + # tdump object, grab tris dynamically + + elif type(arg) is types.InstanceType and ".tdump" in str(arg.__class__): + self.triflag = 2 + self.objextra = arg else: raise StandardError,"unrecognized argument to dump.extra()" diff --git a/tools/python/pizza/gnu.py b/tools/python/pizza/gnu.py index b2d1f55a3d..f6f0167330 100644 --- a/tools/python/pizza/gnu.py +++ b/tools/python/pizza/gnu.py @@ -19,7 +19,7 @@ g.plot(a,b) plot B against A g.plot(a,b,c,d,...) plot B against A, D against C, etc g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc - each plot argument can be a tuple, list, or Numeric vector + each plot argument can be a tuple, list, or Numeric/NumPy vector mplot loops over range(M,N,S) and create one plot per iteration last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors each plot is made from a portion of the vectors, depending on loop index i diff --git a/tools/python/pizza/log.py b/tools/python/pizza/log.py index 04c896c60b..aeca1d8d82 100644 --- a/tools/python/pizza/log.py +++ b/tools/python/pizza/log.py @@ -219,6 +219,8 @@ class log: if self.style == 1: s1 = txt.find(self.firststr) s2 = txt.find("\n--",s1) + if (s2 == -1): + s2 = txt.find("\nLoop time of",s1) pattern = "\s(\S*)\s*=" keywords = re.findall(pattern,txt[s1:s2]) keywords.insert(0,"Step") @@ -270,9 +272,7 @@ class log: s1 = txt.find(self.firststr,start) s2 = txt.find("Loop time of",start+1) - if s2 == -1: - s2 = txt.find("ERROR",start+1) - + if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2 if self.style == 2: s1 = txt.find("\n",s1) + 1 @@ -296,9 +296,6 @@ class log: if txt.find("Loop time of",start) == start: # end of file, so exit eof -= len(txt) - start # reset eof to "Loop" break - if txt.find("ERROR",start) == start: # end of file, so exit - eof -= len(txt) - start # reset eof to "ERROR" - break last = 1 # entire read is a chunk s1 = 0 @@ -324,6 +321,7 @@ class log: word2 = re.findall(pat2,section) words = word1 + word2 self.data.append(map(float,words)) + else: lines = chunk.split("\n") for line in lines: From 6663800ad9b2557c64392f84ee443f9e1289d2a8 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 14 Aug 2015 19:07:16 +0000 Subject: [PATCH 2/4] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13886 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/accelerate_cuda.html | 2 +- doc/doc2/accelerate_gpu.html | 2 +- doc/doc2/accelerate_intel.html | 4 ++-- doc/doc2/accelerate_omp.html | 2 +- doc/doc2/accelerate_opt.html | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/doc2/accelerate_cuda.html b/doc/doc2/accelerate_cuda.html index b8c6ecbab8..0f3017b09b 100644 --- a/doc/doc2/accelerate_cuda.html +++ b/doc/doc2/accelerate_cuda.html @@ -80,7 +80,7 @@ Type "Make.py -h" for help. If run from the src directory, this command will create src/lmp_cuda using src/MAKE/Makefile.mpi as the starting Makefile.machine:

-
Make.py -p cuda -cuda mode=single arch=20 -o cuda lib-cuda file mpi 
+
Make.py -p cuda -cuda mode=single arch=20 -o cuda -a lib-cuda file mpi 
 

 
Or you can follow these two (a,b) steps:
 

diff --git a/doc/doc2/accelerate_gpu.html b/doc/doc2/accelerate_gpu.html
index fcf563e175..b8f2f6705f 100644
--- a/doc/doc2/accelerate_gpu.html
+++ b/doc/doc2/accelerate_gpu.html
@@ -82,7 +82,7 @@ Type "Make.py -h" for help.  If run from the src directory, this
 command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
 starting Makefile.machine:
 

-
Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi 
+
Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi 
 

 
Or you can follow these two (a,b) steps:
 

diff --git a/doc/doc2/accelerate_intel.html b/doc/doc2/accelerate_intel.html
index 2972e989c3..459b314d9f 100644
--- a/doc/doc2/accelerate_intel.html
+++ b/doc/doc2/accelerate_intel.html
@@ -103,8 +103,8 @@ in Section 2.4 of the manual.  Type
 will create src/lmp_intel_cpu and lmp_intel_phi using
 src/MAKE/Makefile.mpi as the starting Makefile.machine:
 

-
Make.py -p intel omp -intel cpu -o intel_cpu -cc icc file mpi 
-Make.py -p intel omp -intel phi -o intel_phi -cc icc file mpi 
+
Make.py -p intel omp -intel cpu -o intel_cpu -cc icc -a file mpi 
+Make.py -p intel omp -intel phi -o intel_phi -cc icc -a file mpi 
 

 
Note that this assumes that your MPI and its mpicxx wrapper
 is using the Intel compiler.  If it is not, you should
diff --git a/doc/doc2/accelerate_omp.html b/doc/doc2/accelerate_omp.html
index d30135f1d1..9514c4ec5e 100644
--- a/doc/doc2/accelerate_omp.html
+++ b/doc/doc2/accelerate_omp.html
@@ -48,7 +48,7 @@ MPI task running on a CPU.
 src/lmp_omp using src/MAKE/Makefile.mpi as the starting
 Makefile.machine:
 

-
Make.py -p omp -o omp file mpi 
+
Make.py -p omp -o omp -a file mpi 
 

 
Or you can follow these steps:
 

diff --git a/doc/doc2/accelerate_opt.html b/doc/doc2/accelerate_opt.html
index a539df5914..3d96b9b511 100644
--- a/doc/doc2/accelerate_opt.html
+++ b/doc/doc2/accelerate_opt.html
@@ -44,7 +44,7 @@ input script.
 src/lmp_opt using src/MAKE/Makefile.mpi as the starting
 Makefile.machine:
 

-
Make.py -p opt -o opt file mpi 
+
Make.py -p opt -o opt -a file mpi 
 

 
Or you can follow these steps:
 


From 2395d650df291ad92c364032e86c376384f51fd3 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Fri, 14 Aug 2015 19:07:30 +0000
Subject: [PATCH 3/4] ''

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13887 f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
 doc/accelerate_cuda.html  | 2 +-
 doc/accelerate_cuda.txt   | 2 +-
 doc/accelerate_gpu.html   | 2 +-
 doc/accelerate_gpu.txt    | 2 +-
 doc/accelerate_intel.html | 4 ++--
 doc/accelerate_intel.txt  | 4 ++--
 doc/accelerate_omp.html   | 2 +-
 doc/accelerate_omp.txt    | 2 +-
 doc/accelerate_opt.html   | 2 +-
 doc/accelerate_opt.txt    | 2 +-
 10 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/doc/accelerate_cuda.html b/doc/accelerate_cuda.html
index f1d45f0937..65183cff2f 100644
--- a/doc/accelerate_cuda.html
+++ b/doc/accelerate_cuda.html
@@ -180,7 +180,7 @@ described in 
-
Make.py -p cuda -cuda mode=single arch=20 -o cuda lib-cuda file mpi
+
Make.py -p cuda -cuda mode=single arch=20 -o cuda -a lib-cuda file mpi
 

 

 
Or you can follow these two (a,b) steps:

diff --git a/doc/accelerate_cuda.txt b/doc/accelerate_cuda.txt
index 43b4d660de..5a6ca4925f 100644
--- a/doc/accelerate_cuda.txt
+++ b/doc/accelerate_cuda.txt
@@ -77,7 +77,7 @@ Type "Make.py -h" for help.  If run from the src directory, this
 command will create src/lmp_cuda using src/MAKE/Makefile.mpi as the
 starting Makefile.machine:
 
-Make.py -p cuda -cuda mode=single arch=20 -o cuda lib-cuda file mpi :pre
+Make.py -p cuda -cuda mode=single arch=20 -o cuda -a lib-cuda file mpi :pre
 
 Or you can follow these two (a,b) steps:
 
diff --git a/doc/accelerate_gpu.html b/doc/accelerate_gpu.html
index 95edb9fd70..eddf4e064c 100644
--- a/doc/accelerate_gpu.html
+++ b/doc/accelerate_gpu.html
@@ -184,7 +184,7 @@ described in 
-
Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi
+
Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi
 

 

 
Or you can follow these two (a,b) steps:

diff --git a/doc/accelerate_gpu.txt b/doc/accelerate_gpu.txt
index bfe9ae7e27..b06e409cd9 100644
--- a/doc/accelerate_gpu.txt
+++ b/doc/accelerate_gpu.txt
@@ -79,7 +79,7 @@ Type "Make.py -h" for help.  If run from the src directory, this
 command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
 starting Makefile.machine:
 
-Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi :pre
+Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre
 
 Or you can follow these two (a,b) steps:
 
diff --git a/doc/accelerate_intel.html b/doc/accelerate_intel.html
index 984302118b..bc04eacace 100644
--- a/doc/accelerate_intel.html
+++ b/doc/accelerate_intel.html
@@ -202,8 +202,8 @@ in Section
 “Make.py -h” for help.  If run from the src directory, these commands
 will create src/lmp_intel_cpu and lmp_intel_phi using
 src/MAKE/Makefile.mpi as the starting Makefile.machine:

-
Make.py -p intel omp -intel cpu -o intel_cpu -cc icc file mpi
-Make.py -p intel omp -intel phi -o intel_phi -cc icc file mpi
+
Make.py -p intel omp -intel cpu -o intel_cpu -cc icc -a file mpi
+Make.py -p intel omp -intel phi -o intel_phi -cc icc -a file mpi
 

 

 
Note that this assumes that your MPI and its mpicxx wrapper
diff --git a/doc/accelerate_intel.txt b/doc/accelerate_intel.txt
index c0cbafa448..8794138933 100644
--- a/doc/accelerate_intel.txt
+++ b/doc/accelerate_intel.txt
@@ -100,8 +100,8 @@ in "Section 2.4"_Section_start.html#start_4 of the manual.  Type
 will create src/lmp_intel_cpu and lmp_intel_phi using
 src/MAKE/Makefile.mpi as the starting Makefile.machine:
 
-Make.py -p intel omp -intel cpu -o intel_cpu -cc icc file mpi 
-Make.py -p intel omp -intel phi -o intel_phi -cc icc file mpi :pre
+Make.py -p intel omp -intel cpu -o intel_cpu -cc icc -a file mpi 
+Make.py -p intel omp -intel phi -o intel_phi -cc icc -a file mpi :pre
 
 Note that this assumes that your MPI and its mpicxx wrapper
 is using the Intel compiler.  If it is not, you should
diff --git a/doc/accelerate_omp.html b/doc/accelerate_omp.html
index 0663e12685..2a78e2f1f1 100644
--- a/doc/accelerate_omp.html
+++ b/doc/accelerate_omp.html
@@ -155,7 +155,7 @@ MPI task running on a CPU.

 -h” for help.  If run from the src directory, this command will create
 src/lmp_omp using src/MAKE/Makefile.mpi as the starting
 Makefile.machine:

-
Make.py -p omp -o omp file mpi
+
Make.py -p omp -o omp -a file mpi
 

 

 
Or you can follow these steps:

diff --git a/doc/accelerate_omp.txt b/doc/accelerate_omp.txt
index 08b9f3c757..9d461f5199 100644
--- a/doc/accelerate_omp.txt
+++ b/doc/accelerate_omp.txt
@@ -45,7 +45,7 @@ To do this in one line, use the src/Make.py script, described in
 src/lmp_omp using src/MAKE/Makefile.mpi as the starting
 Makefile.machine:
 
-Make.py -p omp -o omp file mpi :pre
+Make.py -p omp -o omp -a file mpi :pre
 
 Or you can follow these steps:
 
diff --git a/doc/accelerate_opt.html b/doc/accelerate_opt.html
index 60f1afb2a6..fc5c779528 100644
--- a/doc/accelerate_opt.html
+++ b/doc/accelerate_opt.html
@@ -149,7 +149,7 @@ input script.

 -h” for help.  If run from the src directory, this command will create
 src/lmp_opt using src/MAKE/Makefile.mpi as the starting
 Makefile.machine:

-
Make.py -p opt -o opt file mpi
+
Make.py -p opt -o opt -a file mpi
 

 

 
Or you can follow these steps:

diff --git a/doc/accelerate_opt.txt b/doc/accelerate_opt.txt
index 726f32686f..23e853aec2 100644
--- a/doc/accelerate_opt.txt
+++ b/doc/accelerate_opt.txt
@@ -41,7 +41,7 @@ To do this in one line, use the src/Make.py script, described in
 src/lmp_opt using src/MAKE/Makefile.mpi as the starting
 Makefile.machine:
 
-Make.py -p opt -o opt file mpi :pre
+Make.py -p opt -o opt -a file mpi :pre
 
 Or you can follow these steps:
 

From 21dd53e50d4751dff29f2bf920c5c25ee8be8878 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Fri, 14 Aug 2015 19:09:06 +0000
Subject: [PATCH 4/4] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@13888
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Manual.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/Manual.txt b/doc/Manual.txt
index b0857e6c32..f47482fdf2 100644
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
 
 .. toctree::
    :maxdepth: 2
-   :numbered:
+   :numbered: // comment
    
    Section_intro
    Section_start
@@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
 Indices and tables
 ==================
 
-* :ref:`genindex`
-* :ref:`search`
+* :ref:`genindex` // comment
+* :ref:`search` // comment
    
 END_RST -->