TITLE

Transcription

1 VisBAR Wave Batch v

2 1 VisBAR wave batch Cube Cube PNG Python VTK Cube xyz VTK Cube VTK library.py A VTK 82 B 85 B.1 VisBAR wave batch v0.9 : i

3 2.1 Cube VTK ( ) ( PNG ) ii

4 1 VisBAR wave batch 1.1 VisBAR wave batch Python[1] Input GaussianCube ( Cube ) Cube Cube README VisBAR_wave _batch[*] Python VisBAR_wave _batch VisBAR (VisBAR=Visualization tool with Ball, Arrow, Rod)[*][1] VisBAR_wave _batch [1] ( [2] ) [*] [1] Takeo Hoshi, Yohei Akiyama, Tatsunori Tanaka and Takahisa Ohno, "Ten-million-atom electronic structure calculations on the K computer with a massively parallel order-n theory", J. Phys. Soc. Jpn. 82, , 4pp (2013). [2] Takeo Hoshi, Keita Yamazaki, Yohei Akiyama, " Novel linear algebraic theory and one-hundred-million-atom electronic structure calculation on the K computer ", in press; Preprint ( 1

5 Visualization Tool Kit (VTK)[2] 2 2

6 py Python (1)VisBAR_wave_batch.py VisBAR wave batch (2)formatconvert.py Cube VTK (3)visualize_isosurface.py (4)library.py (5)bond_length.txt (6)visbar_wb_setting_defalt.txt (7)Cube Cube (.cube ) (8)00README_FIRST_JP.txt README ( ) (9)00README_FIRST_EN.txt README ( ) 3

7 2 Cube 2.1 VTK A 1. Python( ) 2. Numpy[3](Python ) 3. VTK Python Wrapper VTK A 1. Python Python2.7.x (Python Windows Installer (Windows binary )) 2. Python2.7 Python(command line) print hello hello Python 4

8 3. Numpy Numpy NumPy/ numpy win32-superpack-python2.7.exe Numpy Python command line import numpy print numpy.matrix([[1,2],[3,4]]) [[1, 2], [3, 4]] 5. VTK VTK ( A ) Python( ver2.7) 1 URL URL VTK 2 3 URL 2 3 URL 1 URL Backup 3 URL 1,VTK win32-py2.7.exe (2,VTK win32.exe [Python2.7]) (3,VTK win32-py2.7.exe) URL 6. sample sphere.py 7. sample sphere.py 3.1 5

9 2.2 Cube VisBAR wave batch Cube [ ] 1. VisBAR wave batch.py Input:[Auto:a, frame by frame:c] PNG a 2. a Cube PNG Cube PNG Python IDLE(Python GUI) 2.1: Cube 6

10 2.3 Cube PNG Cube [ ] 1. Cube 2. VisBAR wave batch.py [Auto:a] 3. Cube PNG 7

11 2.4 Cube [ ] 1. VisBAR wave batch.py Input:[Auto:a, frame by frame:c] c 2. Python IDLE(Python GUI) Visualization Toolkit VTK ( ) VTK ( ) j joystick ( ) t trackball ( ) e Visualization Toolkit w ( s ) s ( ) 3 ( ) r p u a z ( ) png ( image*.png ) (a+ or a+ ) 2.5 8

12 *(1.01)**level level level 1 level 1 level 1 level 1 level 1 level 1 Python command line 9

13 2.5 visbar wb setting defalt.txt 2.4 z visbar wb setting output.txt visbar wb setting.txt 1. VisBAR wave batch.py c z visbar wb setting output.txt 2. customize setting y parallelview customize setting:[on:1,off:=0] On Off 0 customize setting n On y/n VTK Python command line 3. visbar wb setting output.txt z visbar wb setting output.txt visbar wb setting.txt 6. visbar wb setting.txt 7. VisBAR wave batch.py 10

14 visbar wb setting.txt 1 --end setting-- visbar wb setting defalt.txt isovalue 0.02 isovalueminus isoopacity 1.0 outlinecolor Window_size isominusr 1.0 isominusg 0.0 isominusb 0.0 isominusr 1.0 isoplusr 1.0 isoplusg 1.0 isoplusb 0.0 BackGround FocalPoint Position ParallelScale 30.0 ViewUp bond On atom On wave_function On outline On parallel_view On text On --end_setting-- 11

15 isovalue ( ) isovalueminus ( ) isoopacity ( ) outlinecolor (RGB ) (R,G,B)=( , , ) Window size (, ) isominusr RGB R ( ) isominusg RGB G ( ) isominusb RGB B ( ) isoplusr RGB R ( ) isoplusg RGB G ( ) isoplusb RGB B ( ) BackGround (RGB ) (R,G,B)=( , , ) FocalPoint ( ) Position ( ) ParallelScale ( ) ViewUp ( ) bond On (On/Off) atom On (On/Off) wave function (On/Off) outline (On/Off) parallel view parerellview (OnOff) text (On/Off) 12

16 2.6 bond length.txt bond length.txt 1 --end setting-- bond length.txt C C 3.0 C H 2.2 H C 2.2 H H end_setting-- C 6 H 6 C-C C-H H-C H-H 4 ( ) C-H H-C C H Cube 2.7 convert wave function.vtk.txt Cube make atom.xyz.txt Cube XYZ 13

17 3.3.2 log VTK.txt Cube Cube 14

18 3 VisBAR wave batch 3.1 Python 3D VTK Python Python ( ) Python ( ) PC f = open("sample","r") line = f.readline() while line: line = f.readline() if line.find("check") >= 0: print line break f.cloce() sample check Python python 15

19 ( ) 16

20 3.1.2 VTK 3 VTK Python Wrapper URL sample sphere.py import vtk source = vtk. vtkspheresource ( ) source. SetCenter ( 0, 0, 0 ) source. SetRadius ( 8. 0 ) mapper = vtk. vtkpolydatamapper ( ) mapper. SetInput ( source. GetOutput ( ) ) a c t o r = vtk. vtkactor ( ) a c t o r. SetMapper ( mapper ) r e n = vtk. vtkrenderer ( ) ren. AddActor ( a c t o r ) renwin = vtk. vtkrenderwindow ( ) renwin. AddRenderer ( ren ) i r e n = vtk. vtkrenderwindowinteractor ( ) i r e n. SetRenderWindow ( renwin ) i r e n. I n i t i a l i z e ( ) renwin. Render ( ) i r e n. S t a r t ( ) 17

21 3.1: VTK [import vtk] 1 vtk [source = vtk.vtkspheresource()] 2 vtk Sphere sorce [source.setcenter(0,0,0)] 3 sorce Sphere (x,y,z)=(0,0,0) [source.setradius(8.0)] 4 sorce Sphere 8.0 [mapper = vtk.vtkpolydatamapper()] 5 vtkpolydatamapper mapper [mapper.setinput(source.getoutput())] Sphere mapper [actor = vtk.vtkactor()] 7 vtkactor actor [actor.setmapper(mapper)] 8 5,6 mapper actor 18

22 [ren = vtk.vtkrenderer()] 9 vtkrenderer ren [ren.addactor(actor)] 10 actor ren [renwin = vtk.vtkrenderwindow()] 11 vtkrenderwindow renwin [renwin.addrenderer(ren)] 12 renwin ren [iren = vtk.vtkrenderwindowinteractor()] 13 vtkrenderwindowinteractor iren [iren.setrenderwindow(renwin)] 14 iren renwin [iren.initialize()] 15 iren [renwin.render()] 16 renwin [iren.start()] 17 iren 19

23 [ ] sorce Dataset or ( VTK sphere[ ] ) filter sorce mapper sorce filter (actor) actor renderer actor renderwindow actor renderer iren(renderwindowinteractor) VTK 20

24 3.2 VisBAR wave batch.py formatconvert.py visualize isosurface.py library.py 4 Cube VTK xyz VTK ( ) xyz ( ) 3.2: ( ) 3.3: ( PNG ) 21

25 3.2.1 (formatconvert.py) (visualize isosurface.py) PNG 1 Cube (x,y,z) 2 Cube Cube 6 3 VTK x z VTK VTK 5 Cube xyz 4,6,7 (visualize isosurface.py) (visbar wb setting defalt.txt bond length.txt) VTK xyz VTK PNG 22

26 Cube Cube eigen state cube (C 6 H 6 ) HOMO HOMO wavefunction of thermally vibrated C6H E E E E E x,y,z ( ) (40) 4 (80 ) x 5 (80 ) y 6 (80 ) z 7 12 (x,y,z) (x,y,z) 18 23

27 xyz (C 6 H 6 )[3.3.1] Cube xyz 12 HOMO wavefunction of thermally vibrated C6H6 C C C C C C H H H H H H (Cube 1 +2 ) x y z 24

28 3.3.3 VTK (C 6 H 6 )[3.3.1] Cube VTK # vtk DataFile Version 2.0 Probability density for the 3d electron position in a hydrogen atom ASCII DATASET STRUCTURED_POINTS DIMENSIONS ORIGIN SPACING POINT_DATA SCALARS probability_density float LOOKUP_TABLE default ( ) 3 (ASCII BINARY ASCII) 4 ( ) 5 x,y,z 6 (x,y,z) 7 (X, Y, Z) 8 ( ) 9 10 LookUpTable 11 25

29 3.3.4 Cube VTK Cube VTK Cube xyz VTK Cube VTK Cube (x,y,z) 6 z y x F(Mx,My,Mz) F (0, 0, 0) F (0, 0, 1) F (0, 0, 2) F (0, 0, 3) F (0, 0, 4) F (0, 0, 5) F (0, 0, 6) F (0, 0, 7) F (0, 0, 8) F (0, 0, 9) F (0, 0, 10) F (0, 0, 11) F (0, 0, 73) F (0, 0, 74) F (0, 0, 75) F (0, 0, 76) F (0, 0, 77) F (0, 0, 78) F (0, 0, 79) F (0, 0, 80) F (0, 1, 0) F (0, 1, 1) F (0, 1, 2) F (0, 1, 3) F (0, 1, 4) F (0, 1, 5) F (0, 1, 6) F (0, 1, 7) F (0, 1, 8) F (0, 1, 9) F (0, 1, 10) F (0, 1, 11) F (0, 1, 73) F (0, 1, 74) F (0, 1, 75) F (0, 1, 76) F (0, 1, 77) F (0, 1, 78) F (0, 1, 79) F (0, 1, 80) VTK 80 x y z F(Nx,Ny,Nz) F (0, 0, 0) F (1, 0, 0) F (2, 0, 0)... F (79, 0, 0) F (80, 0, 0) F (0, 1, 0) F (1, 1, 0) F (2, 1, 0)... F (79, 1, 0) F (80, 1, 0) F (0, 80, 0) F (1, 80, 0) F (2, 80, 0)... F (79, 80, 0) F (80, 80, 0) F (0, 0, 1) F (1, 0, 1) F (2, 0, 1)... F (79, 0, 1) F (80, 0, 1) F (0, 1, 1) F (1, 1, 1) F (2, 1, 1)... F (79, 1, 1) F (80, 1, 1) F (0, 80, 80) F (1, 80, 80) F (2, 80, 80)... F (79, 80, 80) F (80, 80, 80) Cube Cube VTK... 26

30 3.4 / import os import re import formatconvert as convert convert import visualize_isosurface as view view import vtk vtk Cube pwd = os.getcwd() files = os.listdir(pwd) path( ) out_log = open( log_vtk.txt, w ) log_vtk.txt out_log cnt = 0 Batch_mode = raw_input("input:[auto:a, frame by fram:c]=") 27

31 a Cube PNG c a Cube 1 2 for filenametext in files: files filenametext if filenametext.find(".cube") >= 0:.cube if if filenametext.find(".png") <0:.png if PNG.cube if ( sample.cube.png Cube ) print " " print filenametext Cube out_log.write(filenametext + \n ) if cnt == 0: 0 if 1 2 check_line=convert.cube_vtk(filenametext) filenametext view.vtk(filenametext,batch_mode) filenametext,batch_mode 28

32 cnt +=1 1 elif cnt >= 1: 1 if 1 2 check_line=convert.cube_vtk2(filenametext,check_line) filenametext check_line view.vtk(filenametext,batch_mode) filenametext,batch_mode out_log.close Cube xyz import os import re import library as lib library lib def cube_vtk(filenametext): filenametext f = open(filenametext, r ) filenametext Cube out = open( make_atom.xyz.txt, w ) ( make_atom.xyz.txt, w ) 29

33 Cube 6 cube_list=[] cube_list for j in range(0,6): j 0 5 cube_read = f.readline() 1 cube_read = cube_read.rstrip() 1 cube_read = re.sub("\n","",cube_read) 1 cube_read = re.split(" *",cube_read) 1 cube_list +=[cube_read] 1 cube_list Cube xyz new_cube = int(cube_list[2][1])*-1 cube_list[2][1] xyz - out.write(str(new_cube) + \n ) comment0=len(cube_list[0]) Cube comment1=len(cube_list[1]) Cube 30

34 out.write(" ") for com0 in range(0,comment0): out.write(str(cube_list[0][com0])+ ) for com1 in range(0,comment1): out.write(str(cube_list[1][com1])+ ) out.write(" "+ \n ) Cube (7 19 ) all_atom=[] all_atom for j in range(0,new_cube): (new_cube) atomxyz = f.readline() 1 atomxyz = atomxyz.rstrip() 1 atomxyz = re.sub("\n","",atomxyz) 1 atomxyz = re.split(" *",atomxyz) 1 31

35 all_atom +=[atomxyz] 1 atomxyz (library.py) Cube xyz for k in range(0,int(cube_list[2][1])*-1): for m in range(0,117): library.py (117 ) if lib.library.items()[m][1][0] == int(float(all_atom[k][1])): library.py Cube if out.write(lib.library.items()[m][0]+ ) library.py else: continue if for l in range (3,6): l 3 5 if l==5: l 5 out.write(all_atom[k][l]+ \n ) xyz z else: l 5 out.write(all_atom[k][l]+ ) xyz z Cube xyz 32

36 out.close xyz f.close Cube Cube Cube f = open(filenametext, r ) filenametext Cube out = open( convert_wave_function.vtk.txt, w ) convert_wave_function.vtk.txt Cube check = 0 check 0 check2 = 1 check2 1 for n in range(0,7+int(cube_list[2][1])*-1): Cube f.readline() 1 Cube z L mod L=int(cube_list[5][1])/6 L 33

37 mod=int(cube_list[5][1])%6 6 mod Cube L mod Cube 6 Cube 6 VTK for line in range(0,1): for line1 in f.readlines(): line1 1 check += 1 1 t1=line1.split() t1 if int(cube_list[5][1])/6 +1 == check/check2: Cube_list[5][1] z ( 80) 6 check/check2 if if 6 check2 += 1 check2 if mod == 0: mod 0 i out.write( + \n ) continue elif mod == 1: mod 1 elif 34

38 x0=float(t1[0]) x0 t1[0] out.write( %f %x0+ + \n ) x0 continue elif mod == 2: x0=float(t1[0]) x1=float(t1[1]) out.write( %f %x0+ + %f %x1+ + \n ) continue elif mod == 3: x0=float(t1[0]) x1=float(t1[1]) x2=float(t1[2]) out.write( %f %x0+ + %f %x1+ + %f %x2+ + \n ) continue elif mod == 4: x0=float(t1[0]) x1=float(t1[1]) x2=float(t1[2]) x3=float(t1[3]) out.write( %f %x0+ + %f %x1+/ + %f %x2+ + %f %x3+ + \n ) continue elif mod == 5: x0=float(t1[0]) x1=float(t1[1]) x2=float(t1[2]) x3=float(t1[3]) x4=float(t1[4]) out.write( %f %x0+ + %f %x1+/ + %f %x2+ + %f %x3+ + %f %x4+ + \n ) continue continue x0=float(t1[0]) x1=float(t1[1]) x2=float(t1[2]) x3=float(t1[3]) 35

39 x4=float(t1[4]) x5=float(t1[5]) out.write( %f %x0+ + %f %x1+/ + %f %x2+ + %f %x3+ + %f %x4+ + %f %x5+ ) out.close() f.close() cube VTK f = open( convert_wave_function.vtk.txt, r ) out = open( VTK_out.vtk, w ) VTK total_line=[] total_line mirror = [] mirror for j in range (0,int(cube_list[3][1])): x j all_line=[] all_line for i in range(0,int(cube_list[4][1])): y i line = f.readline() 1 line = line.rstrip() 1 36

40 line = re.sub("\n","",line) 1 line = re.split(" ",line) 1 all_line += [line] 1 all_line total_line += [all_line] all_line total_line VTK x z out.write( # vtk DataFile Version \n ) VTK VTK out.write( Probability density for the 3d electron position in / a hydrogen atom + \n ) out.write( ASCII + \n ) VTK ASCII (ASCII BAINARY ) out.write( DATASET STRUCTURED_POINTS + \n ) STRUCTURED_POINTS out.write( DIMENSIONS + +cube_list[3][1]+ +cube_list[4][1]+/ +cube_list[5][1]+ \n ) eigen_state_ cube.txt (x,y,z )=(80,80,80) out.write( ORIGIN + +cube_list[2][2]+ +cube_list[2][3]+/ +cube_list[2][4]+ \n ) eigen_state_ cube.txt (x,y,z)=( , , ) out.write( SPACING + +cube_list[3][2]+ +cube_list[4][3]+/ +cube_list[5][4]+ \n ) 37

41 eigen_state_ cube.txt (x,y,z )=( , , ) out.write( POINT_DATA + +str(int(cube_list[3][1])*int(cube_list[4][1])*/ int(cube_list[5][1]))+ + \n ) eigen_state_ cube.txt (x 80) (y 80) (z 80)= out.write( SCALARS probability_density float + \n ) out.write( LOOKUP_TABLE default + \n ) LOOKUP_TABLE default for k in range (0,int(cube_list[5][1])): z for j in range (0,int(cube_list[4][1])): y for i in range (0,int(cube_list[3][1])): x if i==(int(cube_list[3][1])-1): x 80 if out.write(total_line[i][j][k]+ \n ) + else: x 80 else out.write(total_line[i][j][k]+ ) + out.close VTK f.close print "end" end Python command line 38

42 return total_line total_line 2 Cube def cube_vtk2(filenametext,check_line): filenametext checl_line f = open(filenametext, r ) filenametext Cube out = open( make_atom.xyz.txt, w ) ( make_atom.xyz.txt, w ) Cube 6 cube_list=[] cube_list for j in range(0,6): j 0 5 cube_read = f.readline() 1 cube_read = cube_read.rstrip() 1 cube_read = re.sub("\n","",cube_read) 1 cube_read = re.split(" *",cube_read) 1 cube_list +=[cube_read] 1 cube_list 39

43 Cube xyz new_cube = int(cube_list[2][1])*-1 cube_list[2][1] xyz - out.write(str(new_cube) + \n ) comment0=len(cube_list[0]) Cube comment1=len(cube_list[1]) Cube out.write(" ") for com0 in range(0,comment0): out.write(str(cube_list[0][com0])+ ) for com1 in range(0,comment1): out.write(str(cube_list[1][com1])+ ) out.write(" "+ \n ) Cube (7 19 ) all_atom=[] all_atom 40

44 for j in range(0,new_cube): (new_cube) atomxyz = f.readline() 1 atomxyz = atomxyz.rstrip() 1 atomxyz = re.sub("\n","",atomxyz) 1 atomxyz = re.split(" *",atomxyz) 1 all_atom +=[atomxyz] 1 atomxyz (library.py) Cube xyz for k in range(0,int(cube_list[2][1])*-1): for m in range(0,117): library.py (117 ) if lib.library.items()[m][1][0] == int(float(all_atom[k][1])): library.py Cube if out.write(lib.library.items()[m][0]+ ) library.py else: continue if for l in range (3,6): l 3 5 if l==5: 41

45 l 5 out.write(all_atom[k][l]+ \n ) xyz z else: l 5 out.write(all_atom[k][l]+ ) xyz z Cube xyz out.close xyz f.close Cube Cube Cube f = open(filenametext, r ) filenametext Cube out = open( convert_wave_function.vtk.txt, w ) convert_wave_function.vtk.txt Cube check = 0 check 0 check2 = 1 check2 1 42

46 for n in range(0,7+int(cube_list[2][1])*-1): Cube f.readline() 1 Cube z L mod L=int(cube_list[5][1])/6 L mod=int(cube_list[5][1])%6 6 mod Cube L mod Cube 6 Cube 6 VTK for line in range(0,1): for line1 in f.readlines(): line1 1 check += 1 1 t1=line1.split() t1 if int(cube_list[5][1])/6 +1 == check/check2: Cube_list[5][1] z ( 80) 6 check/check2 if if 6 43

47 check2 += 1 check2 if mod == 0: mod 0 i out.write( + \n ) continue elif mod == 1: mod 1 elif x0=float(t1[0]) x0 t1[0] out.write( %f %x0+ + \n ) x0 continue elif mod == 2: x0=float(t1[0]) x1=float(t1[1]) out.write( %f %x0+ + %f %x1+ + \n ) continue elif mod == 3: x0=float(t1[0]) x1=float(t1[1]) x2=float(t1[2]) out.write( %f %x0+ + %f %x1+ + %f %x2+ + \n ) continue elif mod == 4: x0=float(t1[0]) x1=float(t1[1]) x2=float(t1[2]) x3=float(t1[3]) out.write( %f %x0+ + %f %x1+/ 44

48 + %f %x2+ + %f %x3+ + \n ) continue elif mod == 5: x0=float(t1[0]) x1=float(t1[1]) x2=float(t1[2]) x3=float(t1[3]) x4=float(t1[4]) out.write( %f %x0+ + %f %x1+/ + %f %x2+ + %f %x3+ + %f %x4+ + \n ) continue continue x0=float(t1[0]) x1=float(t1[1]) x2=float(t1[2]) x3=float(t1[3]) x4=float(t1[4]) x5=float(t1[5]) out.write( %f %x0+ + %f %x1+/ + %f %x2+ + %f %x3+ + %f %x4+ + %f %x5+ ) out.close() f.close() cube VTK f = open( convert_wave_function.vtk.txt, r ) out = open( VTK_out.vtk, w ) VTK total_line=[] total_line mirror = [] mirror 45

49 for j in range (0,int(cube_list[3][1])): x j all_line=[] all_line for i in range(0,int(cube_list[4][1])): y i line = f.readline() 1 line = line.rstrip() 1 line = re.sub("\n","",line) 1 line = re.split(" ",line) 1 all_line += [line] 1 all_line total_line += [all_line] all_line total_line Cube sum_wave = 0 sum_wave 0 for i in range(0,int(cube_list[3][1])): i cube_list[3][1] Cube x for j in range(0,int(cube_list[4][1])): j cube_list[4][1] Cube y 46

50 for k in range(0,int(cube_list[5][1])): k cube_list[5][1] Cube z total=total_line[i][j][k] Cube total check_wave=check_line[i][j][k] Cube check_wave total=float(total) total check_wave=float(check_wave) check_wave sum_wave += total*check_wave sum_wave total check_wave if sum_wave >= 0: sum_wave 0 if print "plus",sum_wave "plus" sum_wave elif sum_wave < 0: sum_wave 0 if print "minus",sum_wave "minus" sum_wave for i in range(0,int(cube_list[3][1])): i cube_list[3][1] Cube x for j in range(0,int(cube_list[4][1])): j cube_list[4][1] Cube y for k in range(0,int(cube_list[5][1])): k cube_list[5][1] Cube z dammy=total_line[i][j][k] dammy 47

51 dammy=float(dammy)*-1 dammy -1 total_line[i][j][k]=str(dammy) total_line dammy else : if print "NG" NG Python command line VTK x z out.write( # vtk DataFile Version \n ) VTK VTK out.write( Probability density for the 3d electron position in / a hydrogen atom + \n ) out.write( ASCII + \n ) VTK ASCII (ASCII BAINARY ) out.write( DATASET STRUCTURED_POINTS + \n ) STRUCTURED_POINTS out.write( DIMENSIONS + +cube_list[3][1]+ +cube_list[4][1]+/ +cube_list[5][1]+ \n ) eigen_state_ cube (x,y,z )=(80,80,80) out.write( ORIGIN + +cube_list[2][2]+ +cube_list[2][3]+/ +cube_list[2][4]+ \n ) eigen_state_ cube (x,y,z)=( , , ) out.write( SPACING + +cube_list[3][2]+ +cube_list[4][3]+/ +cube_list[5][4]+ \n ) eigen_state_ cube (x,y,z )=( , , ) 48

52 out.write( POINT_DATA + +str(int(cube_list[3][1])*int(cube_list[4][1])*/ int(cube_list[5][1]))+ + \n ) eigen_state_ cube (x 80) (y 80) (z 80)= out.write( SCALARS probability_density float + \n ) out.write( LOOKUP_TABLE default + \n ) LOOKUP_TABLE default for k in range (0,int(cube_list[5][1])): z for j in range (0,int(cube_list[4][1])): y for i in range (0,int(cube_list[3][1])): x if i==(int(cube_list[3][1])-1): x 80 if out.write(total_line[i][j][k]+ \n ) + else: x 80 else out.write(total_line[i][j][k]+ ) + out.close VTK f.close print "end" end Python command line 49

53 return total_line total_line 50

54 3.4.3 import os import re from vtk import* VTK import library as lib library lib import math math( ) import numpy as np numpy( ) np def setting_read(): setting_read pwd = os.getcwd() pwd files = os.listdir(pwd) path( ) if "visbar_wb_setting_defalt.txt" in files >= 0: visbar_wb_setting_defalt.txt if setting_file_name="visbar_wb_setting_defalt.txt" setting_file_name visbar_wb_setting_defalt.txt f = open(setting_file_name, r ) visbar_wb_setting_defalt.txt 51

55 a=1 a cnt=0 0 dic={} while True: while findsharp=-1 findsharp -1 line = f.readline() 1 if line.find("--end_setting--") >=0 : --end_setting-- break break while break all_line=[] all_line line = line.replace("\t"," ") line = line.rstrip() line = re.sub("\n","",line) line = re.split(" *",line) line if line[0] == "": 52

56 line if continue continue while if line[0].find("#") >=0: line 1 if continue continue while all_line += line all_line line del all_line[0] 0 for i in range(0,len(all_line)): i all_line if all_line[i].find("#") >=0: all_line if findsharp=i i findsharp if findsharp >=0: findsharp 0 if del all_line[findsharp:] all_line if len(all_line) ==0: all_line if print "Dictionary isn t possible" +" "+ "["+line[0]+"]" Dictionary isn t possible continue while para=[] para 53

57 para += all_line para all_line dic[line[0]]=para line para line[0]:para f.close visbar_wb_setting.txt if "visbar_wb_setting.txt" in files >= 0: visbar_wb_setting.txt if setting_file_name="visbar_wb_setting.txt" visbar_wb_setting.txt setting_file_name f = open(setting_file_name, r ) setting_file_name (visbar_wb_setting.txt) a=1 a 1 cnt=0 cnt 0 dic2={} dic2 while True: while findsharp=-1 findsharp -1 line = f.readline() 1 if line.find("--end_setting--") >=0 : 1 --end_setting-- break 54

58 break while break all_line=[] all_line line = line.replace("\t"," ") line = line.rstrip() line = re.sub("\n","",line) line = re.split(" *",line) line if line[0] == "": line if continue continue while if line[0].find("#") >=0: line 1 if continue continue while all_line += line all_line line del all_line[0] 0 for i in range(0,len(all_line)): i all_line if all_line[i].find("#") >=0: all_line if 55

59 findsharp=i i findsharp if findsharp >=0: findsharp 0 if del all_line[findsharp:] all_line if len(all_line) ==0: findsharp 0 if print "Dictionary isn t possible" +" "+ "["+line[0]+"]" Dictionary isn t possible continue while para=[] para para += all_line para all_line dic2[line[0]]=para line para line[0]:para dic.update(dic2) dic dic2 dic return dic dic read=setting_read() setting_read() read def setting_bond(): setting_bond f = open("bond_length.txt", r ) bond_length.txt 56

60 a=1 a cnt=0 0 dic={} while True: while findsharp=-1 findsharp -1 line = f.readline() 1 if line.find("--end_setting--") >=0 : --end_setting-- break break while break all_line=[] all_line line = line.replace("\t"," ") line = line.rstrip() line = re.sub("\n","",line) line = re.split(" *",line) line if line[0] == "": line if continue 57

61 continue while if line[0].find("#") >=0: line 1 if continue continue while all_line += line all_line line del all_line[0:2] 0,1 for i in range(0,len(all_line)): i all_line if all_line[i].find("#") >=0: all_line if findsharp=i i findsharp if findsharp >=0: findsharp 0 if del all_line[findsharp:] all_line if len(all_line) ==0: all_line if print "Dictionary isn t possible" +" "+ "["+line[0]+"]" Dictionary isn t possible continue while dic[line[0],line[1]]=line[2] line line line[0],line[1]]:line[2] 58

62 f.close bond_length.txt retur dic dic read_bond=setting_bond() setting_bond read_bond setting read() save_step = 0 save_step 0 isovalue=float(read["isovalue"][0]) isovalue setting stableiso=float(read["isovalue"][0]) stableiso setting isovalueminus=float(read["isovalueminus"][0]) isovalueminus setting stableisominus=float(read["isovalueminus"][0]) stableisominus setting level=0 level 0 u png save step def vtk(filenametext,batch_mode): vtk filenametext,batch_mode 59

63 save_step = 0 save_step 0 def usermethod(obj, arg): global save_step save_step global print "usermethod" usermethod print "level =",level,"isovalue=",stableiso,"isovalueminus=",stableisominus level Python command line isosurface.setvalue(0,stableiso) isosurface.setvalue isosurfaceminus.setvalue(0,stableisominus) isosurfaceminus.setvalue renwin.render() renwin Render windowtoimagefilter=vtk.vtkwindowtoimagefilter() windowtoimagefilter vtk.vtkwindowtoimagefilter() windowtoimagefilter.setinput(renwin) windowtoimagefilter renwin windowtoimagefilter.update() windowtoimagefilter pngwriter=vtk.vtkpngwriter() pngwriter vtk.vtkpngwriter() pngwriter.setinput(windowtoimagefilter.getoutput()) pngwriter windowtoimagefilter pngwriter.setfilename("image"+ str(save_step) +".png") image+ +.png 60

64 pngwriter.write() pngwriter Write() save_step += 1 save_step 1 setting read setting def setting_write(): setting_write isosurface.setvalue(0,stableiso) isosurface.setvalue isosurfaceminus.setvalue(0,stableisominus) isosurfaceminus.setvalue renwin.render() renwin Render out = open("visbar_wb_setting_output.txt", w ) visbar_wb_setting_output.txt out.write( isovalue + + str(isovalue*(1.01**level)) + \n ) isovalue out.write( isovalueminus + + str(isovalueminus*(1.01**level)) + \n ) isovalueminus out.write( isoopacity + + \ str(isosurfaceactor.getproperty().getopacity()) + \n ) isoopacity out.write( outlinecolor + + str( outlineactor.getproperty().getambientcolor()[ + + str( outlineactor.getproperty().getambientcolor()[ + + str( outlineactor.getproperty().getambientcolor()[ outlinecolor RGB out.write( Window_size + + str(renwin.getsize()[0])\ + + str(renwin.getsize()[1])+ \n ) Window_size (x,y) 61

65 out.write( isominusr + +str(isominusr)+ \n ) isominusr RGB R out.write( isominusg + +str(isominusg)+ \n ) isominusg RGB G out.write( isominusb + +str(isominusb)+ \n ) isominusb RGB B out.write( isoplusr + +str(isoplusr)+ \n ) isoplusr RGB R out.write( isoplusg + +str(isoplusg)+ \n ) isoplusg RGB G out.write( isoplusb + +str(isoplusb)+ \n ) isoplusb RGB B out.write( BackGround + +str(ren.getbackground()[0]) + +str(ren.getbackground()[1]) + +str(ren.getbackground()[2])+ \n ) BackGround RGB out.write( FocalPoint + +str(camera.getfocalpoint()[0]) + +str(camera.getfocalpoint()[1]) + +str(camera.getfocalpoint()[2])+ \n ) FocalPoint FocalPoint out.write( Position + +str(camera.getposition()[0]) + +str(camera.getposition()[1]) + +str(camera.getposition()[2])+ \n ) Position out.write( ParallelScale + +str(camera.getparallelscale())+ \n ) ParallelScale ParallelScale out.write( ViewUp + +str(camera.getviewup()[0]) + +str(camera.getviewup()[1]) + +str(camera.getviewup()[2])+ \n ) ViewUp ViewUp more_setting = raw_input("customize_setting:[yes:y, No:n]=") y 62

66 n more_setting all_parts=["bond","atom","wave_function","outline","parallel_view","text"] all_parts isosurface.setvalue(0,stableiso) isosurface.setvalue isosurfaceminus.setvalue(0,stableisominus) isosurfaceminus.setvalue renwin.render() renwin Render if more_setting == "y": more_setting y if for parts in all_parts: all_parts parts parts_setting = raw_input(parts +"_setting:[on:1, Off:0]=") On/Off On 1 Off 0 if parts_setting == "1": parts_setting 1 if out.write(parts + " " + "On" +"\n") On print parts + " " + "On" On print " " elif parts_setting == "0": parts_setting 0 if out.write(parts + " " + "Off" +"\n") Off print parts + " " + "Off" 63

67 Off print " " elif more_setting =="n": more_setting n if for parts in all_parts: all_parts parts out.write(parts + " " + "On" +"\n") On more_setting n On out.write( --end_setting-- + \n ) --end_setting-- out.close visbar_wb_setting_output.txt StructuredPoints( ) VTK out.vtk reader = vtkstructuredpointsreader() reader vtkstructuredpointsreader() StructuredPoints reader.setfilename("vtk_out.vtk") VTK_out.vtk outline = vtkoutlinefilter() outline vtkoutlinefilter() outline.setinputconnection(reader.getoutputport()) outline reader 64

68 outlinemapper = vtkpolydatamapper() outlinemapper vtkpolydatamapper() outlinemapper.setinputconnection(outline.getoutputport()) outlinemapper outline outlineactor = vtkactor() outlineactor vtkactor() outlineactor.setmapper(outlinemapper) outlineactor outlinemapper outlineactor.getproperty().setcolor(float(read["outlinecolor"][0]), float(read["outlinecolor"][1]), float(read["outlinecolor"][2])) outlineactor RGB (R,G,B) setting ( ) isominusr=float(read["isominusr"][0]) RGB R setting isominusg=float(read["isominusg"][0]) RGB G setting isominusb=float(read["isominusb"][0]) RGB B setting isoplusr=float(read["isoplusr"][0]) RGB R setting isoplusg=float(read["isoplusg"][0]) RGB G setting isoplusb=float(read["isoplusb"][0]) RGB B setting lut=vtkcolortransferfunction() lut 65

69 lut.addrgbpoint(-0.1,isominusr,isominusg,isominusb) -0.1 RGB(isominusR,isominusG,isominusB) lut.addrgbpoint(-0.075,isominusr,isominusg,isominusb) lut.addrgbpoint(-0.05,isominusr,isominusg,isominusb) lut.addrgbpoint(-0.025,isominusr,isominusg,isominusb) lut.addrgbpoint(-0.001,isominusr,isominusg,isominusb) lut.addrgbpoint(0,1,0,0) lut.addrgbpoint(0.001,isoplusr,isoplusg,isoplusb) lut.addrgbpoint(0.025,isoplusr,isoplusg,isoplusb) lut.addrgbpoint(0.05,isoplusr,isoplusg,isoplusb) lut.addrgbpoint(0.075,isoplusr,isoplusg,isoplusb) lut.addrgbpoint(0.1,isoplusr,isoplusg,isoplusb) global global isovalue isovalue global global isovalueminus isovalueminus global isosurface = vtkcontourfilter() isosurface vtkcontourfilter() isosurface.setinputconnection(reader.getoutputport()) isosurface reader isosurface.setvalue(0,isovalue) iosurface isosurfacemapper = vtkpolydatamapper() isosurfacemapper vtkpolydatamapper() isosurfacemapper.setlookuptable(lut) isosurfacemapper lut 66

70 isosurfacemapper.setinputconnection(isosurface.getoutputport()) isosurfacemapper isosurface isosurfaceactor = vtkactor() isosurfaceactor vtkactor() isosurfaceactor.setmapper(isosurfacemapper) isosurfaceactor isosurface isosurfaceactor.getproperty().setopacity(float(read["isoopacity"][0])) setting isosurfaceminus = vtkcontourfilter() isosurfaceminus.setinputconnection(reader.getoutputport()) isosurfaceminus.setvalue(0,isovalueminus) isosurfaceminusmapper = vtkpolydatamapper() isosurfaceminusmapper.setlookuptable(lut) isosurfaceminusmapper.setinputconnection(isosurfaceminus.getoutputport()) isosurfaceminusactor = vtkactor() isosurfaceminusactor.setmapper(isosurfaceminusmapper) isosurfaceminusactor.getproperty().setopacity(float(read["isoopacity"][0])) ren = vtkrenderer() ren vtkrenderer() ren.setbackground(float(read["background"][0]), float(read["background"][1]), float(read["background"][2])) setting xyz 67

71 f=open( make_atom.xyz.txt, r ) xyz atom_list=[] atom_list number=f.readline() number comment=f.readline() comment for j in range(0,int(number)): number( ) atom = f.readline() 1 atom = atom.rstrip() 1 atom = re.sub("\n","",atom) 1 atom = re.split(" *",atom) 1 atom_list +=[atom] 1 atom_list f.close xyz xyz Sphere for k in range(0,int(number)): # create source source0 = vtkspheresource() 68

72 source0 vtkspheresource() vtkspheresource() sphere( ) source0.setcenter(float(atom_list[k][1]),float(atom_list[k][2]),/ float(atom_list[k][3])) source0.setradius(float(lib.library[atom_list[k][0]][1])) source0.setthetaresolution(15) ( ) source0.setphiresolution(15) ( ) # mapper mapper0 = vtkpolydatamapper() mapper0 vtkpolydatamapper() mapper0.setinput(source0.getoutput()) mapper0 sorce() # actor actor0 = vtkactor() actor0 vtkactor() actor0.setmapper(mapper0) actor0 mapper0 actor0.getproperty().setcolor(lib.library[atom_list[k][0]][2][0]/255,/ lib.library[atom_list[k][0]][2][1]/255,lib.library[atom_list[k][0]][2][2]/255) actor0 library.py RGB if read["atom"][0] == "On": atom On actor0 ren.addactor(actor0) ren actor0 69

73 all_atom=atom_list atom_list all_atom for i in range(0,int(number)-1): i 0 (number)-1 for j in range(i+1,int(number)): j i+1 number all_atom[i][1]=float(all_atom[i][1]) all_atom x all_atom[i][2]=float(all_atom[i][2]) all_atom y all_atom[i][3]=float(all_atom[i][3]) all_atom z all_atom[j][1]=float(all_atom[j][1]) all_atom x all_atom[j][2]=float(all_atom[j][2]) all_atom y all_atom[j][3]=float(all_atom[j][3]) all_atom z length = ((all_atom[j][1] - all_atom[i][1])**2.0\ +(all_atom[j][2] - all_atom[i][2])**2.0\ +(all_atom[j][3] - all_atom[i][3])**2.0)**0.5 if length <= float(read_bond[all_atom[i][0],all_atom[j][0]]): bond_length length if radius=0.1 radius 0.1 res=10 res 10 axis=[all_atom[i][1]-all_atom[j][1],\ 70

74 all_atom[i][2]-all_atom[j][2],all_atom[i][3]-all_atom[j][3]] pos=[(all_atom[i][1]+all_atom[j][1])/2.0,(all_atom[i][2]+all_atom[j][2]) height=math.sqrt(axis[0]**2+axis[1]**2+axis[2]**2) theta = math.acos(axis[1] / np.linalg.norm(axis)) v = np.array([axis[2], 0, -axis[0]]) v [axis[2], 0, -axis[0] cylinder = vtkcylindersource() cylinder vtkcylindersource() cylinder.setresolution(res) cylinder.setheight(height) cylinder.setradius(radius) mapper = vtkpolydatamapper() mapper vtkpolydatamapper() mapper.setinput(cylinder.getoutput()) mapper cylinder.getoutput() actor = vtkactor() actor vtkactor() actor.setmapper(mapper) actor mapper actor.rotatewxyz(theta / math.pi * 180, v[0], v[1], v[2]) actor 71

75 actor.setposition(pos) actor position if read["bond"][0] == "On": bond On if ren.addactor(actor) actor camera=vtkcamera() camera vtkcamera() camera.setfocalpoint(float(read["focalpoint"][0]), float(read["focalpoint"][1]), float(read["focalpoint"][2])) camera setting camera.setposition(float(read["position"][0]), float(read["position"][1]), float(read["position"][2])) camera setting (x,y,z) camera.computeviewplanenormal camera ComputeViewPlaneNormal camera.setparallelscale(float(read["parallelscale"][0])) parallelscale setting camera.setviewup(float(read["viewup"][0]), float(read["viewup"][1]), float(read["viewup"][2])) camera camera.usehorizontalviewangleoff camera ren.setactivecamera(camera) 72

76 ren camera if read["parallel_view"][0] == "On": parallel_view On if ren.getactivecamera().parallelprojectionon() On Window txt = vtk.vtktextactor() txt vtk.vtktextactor() txt.setinput(comment) txt comment txtprop=txt.gettextproperty() txtprop txt.gettextproperty() txtprop.setfontfamilytoarial() Arial txtprop.setfontsize(16) txtprop.setcolor(0,0,0) txt.setdisplayposition(10,450) comment2=filenametext comment2 Cube txt2 = vtktextactor() txt2 vtktextactor() txt2.setinput(comment2) txt2 comment2 txtprop2=txt2.gettextproperty() txtprop2 GetTextProperty() 73

77 txtprop2.setfontfamilytoarial() Arial txtprop2.setfontsize(10) txtprop2.setcolor(0,0,0) ren.addactor(txt2) txt2 Actor text_representation = vtktextrepresentation() vtktextrepresentation() text_representation text_representation.getpositioncoordinate().setvalue(0.05, 0.85) text_representation.getposition2coordinate().setvalue(0.8, 0.1) text_widget = vtktextwidget() vtktextwidget() text_widget text_widget.setrepresentation(text_representation) text_widget.setrepresentation text_representation if read["outline"][0] == "On": outline On if ren.addactor(outlineactor) ren outline if read["wave_function"][0] == "On": wave_function On if ren.addactor(isosurfaceactor) 74

78 ren isosurfaceactor ren.addactor(isosurfaceminusactor) ren isosurfaceminusactor renwin = vtkrenderwindow() renwin vtkrenderwindow() renwin.setwindowname("visbar wave batch") renwin VisBAR wave batch renwin.setsize(float(read["window_size"][0]), float(read["window_size"][1])) Window. setting renwin.addrenderer(ren) renwin ren def Keypress(obj, event): global isovalue,isovalueminus,level,stableiso,stableisominus isovalue,isovalueminus,level,stableiso,stableisominus key = obj.getkeysym() key obj.getkeysym() if key == "4": 4 level +=1 level 1 stableiso = isovalue*(1.01**level) isovalue 1.01 lebel stableiso elif key == "5": 75

79 level -=1 stableiso = isovalue*(1.01**level) elif key == "6": level +=1 stableisominus = isovalueminus*(1.01**level) elif key == "7": level -=1 stableisominus = isovalueminus*(1.01**level) elif key == "1": level +=1 stableiso = isovalue*(1.01**level) stableisominus = isovalueminus*(1.01**level) elif key == "2": level -=1 stableiso = isovalue*(1.01**level) stableisominus = isovalueminus*(1.01**level) elif key == "z": setting_write() setting setting print "level =",level,"isovalue=",stableiso,"isovalueminus=",stableisominus level Python command line isosurface.setvalue(0,stableiso) isosurface.setvalue isosurfaceminus.setvalue(0,stableisominus) isosurfaceminus.setvalue renwin.render() renwin Render if Batch_mode == "c" : Batch_mode c if 76

80 w2if = vtkwindowtoimagefilter() vtkwindowtoimagefilter() w2if w2if.setinput(renwin) w2if renwin writer = vtkpngwriter() vtkpngwriter() writer writer.setinput(w2if.getoutput()) writer w2if writer.setfilename(str(filenametext)+".png") Cube.png writer.write() writer print "mode c" Python command line c iren = vtkrenderwindowinteractor() iren vtkrenderwindowinteractor() iren.addobserver("userevent", usermethod) png iren iren.setrenderwindow(renwin) iren renwin iren.addobserver("keypressevent", Keypress) iren text_widget = vtktextwidget() vtktextwidget() text_widget text_widget.setrepresentation(text_representation) text_widget.setrepresentation text_representation text_widget.setinteractor(iren) text_widget.setinteractor iren 77

81 text_widget.settextactor(txt) text_widget txt text_widget.selectableoff() if read["text"][0] == "On": text On if text_widget.on() text_widget iren.initialize() iren Initialize() iren.start() VTK elif Batch_mode == "a" : Batch_mode a if if read["text"][0] == "On": text On if ren.addactor(txt) actor w2if = vtkwindowtoimagefilter() vtkwindowtoimagefilter() w2if w2if.setinput(renwin) w2if renwin writer = vtkpngwriter() vtkpngwriter() writer writer.setinput(w2if.getoutput()) writer w2if writer.setfilename(str(filenametext)+".png") Cube.png 78

82 writer.write() writer print "mode a" Python command line a else : if a else print "mode else" Python command line mode else 79

83 3.4.4 library.py H Ca 118 Python H :[1,0.37,(0.,0.,255.)] H :[1,0.37,(0.,0.,255.)]= :[,,( RGB )] # -*- coding: cp932 -*- library={ H :[1,0.37,(0.,0.,255.)], He :[2,1.5,(0.,255.,0.)], Li :[3,1.52,(82.,82.,255.)], Be :[4,1.13,(128.,0.,255.)], B :[5,0.9,(230.,230.,10.)], C :[6,0.77,(80.,80.,80.)], N :[7,0.53,(255.,128.,0.)], O :[8,0.61,(255.,0.,128.)], F :[9,0.71,(0.,255.,128)], Ne :[10,1.59,(70.,255.,70.)], Na :[11,1.86,(122.,122.,255.)], Mg :[12,1.6,(128.,64.,192.)], Al :[13,1.43,(255.,210.,0.)], Si :[14,1.17,(120.,120.,120.)], P :[15,1.09,(192.,128.,64.)], S :[16,1.02,(192.,64.,128.)], Cl :[17,1.01,(64.,192.,128.)], Ar :[18,1.91,(140.,255.,140.)], K :[19,2.26,(160.,160.,255.)], Ca :[20,1.97,(128.,80.,150.)], 80

84 [1] Python ( ) [2] Visualization Tool Kit (VTK ) [3] Numpy (Numpy ) 81

85 A VTK 1 VTK VTK < > DELL VOSTRO3350 Windows Professional OS32bit servicepack1 WindowsUpdate Python Visual Studio Express 2012 for Windows Desktop VTK vtkdata zip CMake(cmake win32-x86.exe) C++ gfortran < > Linux 4. VTK Python 3D 82

86 Windows VTK Windows Visual Studio VTK Python < > ( ) 1. VTK C:/Users/damp-tottori/Desktop/VTK yamazaki D 2. VTK ( VTK vtk zip 3. VTK vtkdata zip 4. CMake VTK (VTK5.10.1) C:/Users/damp-tottori/Downloads/vtk C:/Users/damptottori/Desktop/vtkBuild Yes 6. Configure Visual Studio11 compiler native Finish CMAKE MAKE PROGRAM MAKE PROGRAM NOT FOUND C:/Windows/Microsoft.NET/Framework/v /MSBuild.exe Configure 7. Advanced( ) BUILD SHARED LIBS check CMAKE CONFIGURATION TYPES Release CMAKE INSTALL PREFIX C:/VTK VTK DATA ROOT C:/VTK/vtkdata VTK WRAP PYTHON check CMAKE LINKER NOT FOUND C:/Program Files/Microsoft Visual Studio 11.0/VC/bin/link.exe COVERAGE COMMAND NOT FOUND C:/Program Files/gfortran/bin/gcov.exe 83

87 8. Configure 9. VTK USE TK check Configure Configure 10. Configure Generate VTK.sln vtkbuild cmake 11. vtkbuild VTK.sln Microsoft Visula Studio Visual Studio Solution Explorer ALL BUILD 13. ALL BUILD Solution Explorer RUN TESTS 14. Solution Explorer INSTALL Python 15. Python VTK Python Python C:/Python27/Lib/site-packages VTK Python VTK (C:/Users/damp-tottori/Desktop/VTK yamazaki Download) /lib/site-packages C:/Python27/Lib/site-packages vtk.pth C:/Users/damp-tottori/Desktop/VTK yamazaki Download packages 16. C:/Users/damp-tottori/Desktop/VTK yamazaki Download/bin C:/Users/damp-tottori/Desktop/VTK yamazaki Download/lib/site-packages vtk 17. Python import vtk < > C:\Program Files INSTALL VisualStadio < > C++ C++ C++ 84

88 B B.1 VisBAR wave batch v0.9 : Cube Cube PerspectiveView ProjectionView Cube Log 85

89 86