応用分子動力学計算プログラム RYUDO 取扱説明書
Contents
1.2. 3 E E
3. v
4. 2
5. F i gt 13 atom 1 2 3 4 1 MgO FezO
6. defLrd atom 7 M defrd step 3 0
7. defird step 1 ryudo c Ver 1 set rd 23 58 ryudo c
8. set rd km s 3 E E
9. cutoff 2 OS NO 8B 0 5 ki D 0 RYUDO Da 8 ri H parr 3 1 1 Harmonic 140 0 kcal moll 1 0 kJ m 2moll 2 70 A Di UFF EE kJ moll kJ m mol pm
10. 100 1000 10 000step 10 100
11. Ver 1 10 velrd twl rd move move Ver 1 11 move 43 7 6
12. 1 1 Gndexy MSD atom nature index x y z indexy MSD Xy Xz 2 xyz
13. 55 5000 step 10000 2 New RYUDO 2 1 defird ryudo defl atom 2 run
14. 1500 pmj defrd cutoff a b c NRN 3 cu cutoff CVFF 1
15. rdmov Ver RYUDO end rd X Y Z m 69 gcc 0 0 rdmov math end rd rdmov
16. 1 MD RYUDO MD MD RYUDO
17. ryujim d3 dion ne jp miura aki che tohoku ac jp RYUDO RYUDO NEW RYUDO RYUDO RYUDO rdset
18. RYUDO RYUDO RYUDO PR 2
19. 20 RYUDO 1step
20. 0 1 m 0 1 m 0 7 2 RYUDO 40 defrrd
21. 1 temp cr press or RYUDO 1 ryudo def RYUDO def rd def rd
22. bp 21 5 set rd set rd 1 gt 3 W rdset RYUDO E xtaldata dat set rd 6 set rd RYUDO rdset rst P1 Accelrys Cerius2 xtl COLORS xtal mdy 1
23. 4 defrd def rd ryudo def 1 20 1 title benzen on Fe203 surface 2 step 100000 0 50 fs 10 3 1 disp 100 1000 5000 0 yz SI 4 files 100 1000 1000 0 0 0 5 cutoff 1500 pm 500 pm 32 6 ewald 6 4 14 0 00027 pm 7 temp 300 0 K 1 0 K 10 10 8 press 1 000 GPa 1 000 GPa fix 1 9 periodic on 10 atom 11 1 1 1 0 0 0 11 2 2 2 0 0 0 3 3 3 0 0 0 4 4 4 0 0 0 index 12 1 C 100 4 0 2 2 H 50 6 0 3 0 120 5 0 4 Fe 70 2 0 hature 13 1 12 01 0 10 LJ 29687 3 kcalA 12 mol 132 70 kcalA 6 mol 13 2 1 01 0 10 LJ 71 4 kcalA 12 mol 32 87 kcalA 6 mol 3 16 00 2 00 Busing 1 629 A 0 085 A 4 55 85 3 00 Busing 1 207 A 0 080 A Dair table 14 00 LJ 14 00 Busing 13 Morse 12 00 kcal mol 1 980 1 A 1 780 A 24 Morse 24 00 kcal mol 1 980 1 A 2 130 A 11b
24. step 11 set rd set rd set rd set rd
25. step 1 step 10 10step 10step 20step 30step 10 step MD step step step 10
26. or cr or Too short 0 1A Too short Warning nn table over flow
27. 3 step MD 1 0 1 RYUDO 1 fs 10 5 1 3 0 4 mi 4 disp
28. 7 rdsrf E 3 bond 3 E E 3 E 64 define B 1 7
29. 3 4 N N Ewald Ewald Es gt periodic Ewald 1 ewald e 1 o 2
30. 7 7 am RYUDO set rd set rd set rd 1 0 0 0 5000 0 5000 0 5000 0 1234 0 2345 0 3456 1 0 0 ad 0 5000 0 5000 0 8000 0 0000 0 0000 1 0000 3
31. RYUDO RYUDO def rd def rd RYUDO 2 title def rd title 72 2
32. defird single move single 1 2 move 1 0 pm single move single move atom set rd move x y z pm 10 Pm Ver 1 05 pm
33. rduni Ver 1 01 rst RYUDO gt 2 FE 0 JJ 1 rst gcc rduni c o rduni math rduni rst 1 rst 2
34. 2 1 3 3 2 4 4 Torsion 2 0 3 b m o a 1 Ver 1 17a 0 4
35. RYUDO Ewald 0 Bwald Coulomb Coulomb pair 0 0 Coulomb nature nature nature i
36. x y z 1 move 1 0 pm 0 0 1 pm 0 0 5 0 pm 0 move x y z x y z x y z pm 1step 1 0pm step 0 1pm 5 0pm 0
37. b m 0 a b 2 3 m 3 o 1 0 3 Ver 1 2 01 set rd bonded 3 RYUDO pair t
38. 6 1 8 part 1 1 Numeric flename f ename lt 1 1 m
39. 2 def rd single single 5 horiz Zz 0 2 hpot dat 1 2 horiz 3 lt y 4 5 e axis OU e separate e 0 4 0 3 e
40. 0 0 N 1 0e 10 N N E 1 1 1x10 N 42 x 1 0 0 0 force x y z x z T x force x 1 0x10 N 0 y 1 1 0x10 IN 7 5 RYUDO
41. x y x y 2 km s 8 H RYUDO 90 00 90 00 90 00 cond 3 def rd temp 2 set rd part
42. K C KJ step Ver 0 85 RYUDO Ver 0 86 10 Ver 0 85 def rd 1
43. 0 0 3 table G k 1 2 j 2 Torsion 4 table G k D 1 2 i 1 2 RYUDO
44. 1 1 RYUDO J set rd E set rd set rd IXDORTO car rdset ryudo set 1 00 title aXIS cond elem wr bond COF OS Dart cc wo a 22 99 0 3728000 0 1272000 0 6272000 0 8728000 0 6272000 0 8728000
45. 6 1 9 2 H H H O 0 O H H en B Al 7 A exp F7 G 3 fo 4 184 6 022e23 1e3 7 62177 1 A2 G 1 45251 A H O U i r l exp Dr 4 1 exp Fr A 36 1345 A B 18 C 40 1 A amp A 72 269 A B 6 361637e 92 C 9 19912 D 40 1 A E G 12 08471 O O B exp D 4 p A 144 538 A B 6 862097675e 85 1 5 1 A2 G 4 5 A gp D exp F r G C 8 6591 D 4
46. x y z rdsum filename elementNo x y z filename pos rd velrd for rd tps rd tvlrd tps rd elementNo setrd elem x y z 1 set rd knd rd valrd 1 1
47. end N 3 Step Temp 100 370 9 278 4 200 431 4 334 0 300 439 8 274 2 3700 460 3 285 5 3800 319 2 297 9 3900 381 4 268 3 4000 325 6 303 9 LoTemp HiTemp LowEnergy J 524 4 6 0984449e 20 455 1 1 5301740e 19 492 1 6 5430227e 19 477 6 8 6984698e 20 481 6 6 1897632e 21 577 4 1 5795278e 19 451 5 8 3655205e 21 HighEnergy J 1 0929429e 19 3 2068997e 19 3 6493591e 20 1 4413814e 19 4 6184647e 20 2 5398951e 19 1 4247757e 19 LowEnergyS J 0 0000000e 00 0 0000000e 00 0 0000000e 00 2 4134119e 18 3 0872629e 18 2 8283404e 18 3 5672638e 18 HighEnergyS J 0 0000000e 00 0 0000000e 00 0 0000000e 00 1 8054827e 18 9 1692270e 19 1 1536329e 18 1 0859657e 18 defrd text 3
48. o0 m m 4 a defird Ver 1 24 defrd b n 2 3 Ver 1 25 set rd bonded
49. 3 Out of Plane G k 1 6 4 1 Out of Plane MD 1 cos H n gt zo H n zo n 1 0 tetra 6 4 1 6 b Plane 1 400 kcal moll 1 0 0 0 Plane kJ moll 3 CC _
50. NZ RYUDO lt RYUDO RYUDO
51. part 4 d a 0 23 gt bond bondon dat end rd end rd set rd
52. ww 7 4 RYUDO def rd single single 1 single N Ver 1 06 1 gt 1 0x10 N 2 force Torce 0 8 ML te
53. 2 pm ewald 6 4 14 0 00027 ewald 11 4 50 0 00027 ewald 14 4 74 0 00027 ewald 23 5 13 0 00027 ewald 29 5 72 0 00027 1 0 Ewald 0 RYUDO Ewald 1 4 4 Torsion
54. kJ moll pm pm 6 2 2 SW 2 3 RYUDO Ui 2 Us 3 4 et x x Xj dA 2 Uk ES Xd XA 3 x o x rm 0o xg rk o U a 0 Ui x gt a xr gt a 0 RYUDO SW pair trio 2 3 pair 1 1 SW 24 47e 19 0 6022 4
55. end car xt set rd Structure0 31 elem E set rd def rd rst TRIBOSIM MSPORT 2 Cerius2 rdset au 3 Sm car 9 Car car 2 E E set rd rd set rd step data
56. 39 6 2 RYUDO 3 6 2 1 Unit 3 j j j jk 70 7 70 7 BE H 90 0 exp exp H 9 r s 6 r j m trio 1 2 1 Unit 30 0 kcal moll 60 0 deg 1 70 A 1 0 A
57. tH 41 atom autode autodel z 0 0 8 x x y y z z lt Ver 1 26m Ver 1 25 a Ver 1 26n Rg lt set rd 2
58. f NBW RYUD O CO E NEW E 2 RYUDO Linux RYUDO
59. Ewald Ewald 1 4 NS 4 CVFF BEwald ewald 4 bondfr 4 Ver 1 23
60. RYUDO 32bit Linux 2GB 64bit Linux 2GB 7 12 Ver 1 10 Ver 1 18h 48 tps rd pos rd 10 RYUDO MSD 1
61. RYUDO defrd fes text files text 100 100 100 tps rd tvl rd tfr rd step OS
62. 2 nature set rd Ver 1 11c atom atom 3 Ver 1 11d atom E 0
63. make make ryudo bin gcc UNIX RYUDO ANSI cc makefile CC gcc CC cc 0PT c ansi Wall make
64. 3 2 1 EE Ewald 0 3 E H RYUDO Ewald a nature 32 1 2 Coulomb 1 00 2 00 e Coulomb 2 2 cutoff cutoff
65. val rd MSD 12 index 16 RYUGA
66. E ryudo c ryudo c SI MXDORTO cnd rd set rd end rd PATH H
67. parr Busing Busing 3 E BEwald parr E F H Coulomb pair Busing 14 2 2
68. CVFF Ewald ewald 4 bondfr Bond Free Ver 1 23 8 temp RYUDO
69. defrd b 19 1 2 3 _ Torsion E CVFF Morse Angle E RYUDO Out of Plane 4 Torsion 4
70. tmp rd def rd pos rd fles 5 1 16bit 8bit 1 1 8bit AR ww MR Sy K E 16bit 8bit 8bit tmp rd defrd
71. Ver 1 23 0 0 1 0 1 0 Ver 1 24 0 0 1 0 set rd 0 0 1 0 Ver 1 23 0 0 1 0 end rd Ver 1 24 0 0 1 0 end rd set rd end rd val rd aXis 2 62000000e 09 2 35600000e 09 7 00000000e 09 90 0 9
72. rdmsp Ver 1 03a TRIBOSIM MSPORT RYUDO file05 dat def rd bondon dat bnd rd gcc rdmsp c o rdmsp math fle05 dat bondon dat rdmsp 0 defrd bndrd bnd rd RYUDO bondon dat Iryudo bnd 0 87 1 1 1 2 Ver 0 87 RYUDO bondon dat bonded
73. 0 LJ RYUDO LJ Ver 1 23 LJ2 1 1 LJ2 50 00 2 74 1 D 2 ry kJ mol A nature LJ D r D r m D r nature pair nature LJ AB g o D r LJ
74. RYUDO NEW RYUDO NEW RYUDO RYUDO NEW RYUDO RYUDO NEW RYUDO RYUDO
75. nature Angell 1 16 00 2 00 Angell 8 0 407 1 420 3 92 1 86 10 Angell nm bi ci ei 1 N pair Aij bitbj oc ir co j Cij Di nature E 6 1 4 Morse RYUDO Morse H Ej D lexp 28 r r 2exp 8 r r 29 Di 8 a Morse 3
76. Morse Discover NH Sh 39 OH LJ CVFF 0 5 fs 0 1 fs 7 RYUDO
77. detrd single single single atom index 7 1 RYUDO defLrd atom atom 1 1 1 0 0 0 2 2 2 0 0 0 X 1 2 0 0 K
78. unsigned long int 32bi 65536 N N RYUDO defi h efine FBT_MODE 2 1 RYUDO 65536 512MB defi h define FBT_MODE 0 2
79. def rd set rd 1CPU RYUDO NO E ns 2 CPU jw 1 2 ee RYUDO
80. les 5 H pos rd pos2 rd RYUDO N 1 2 5 2 x y z 3 5 3 pN 16bit for rd for2 rd 10000 0 9999 4 16bit 8bit 8bit H 32768 32767pN 5 8bit 1 1 16bit for rd for2 rd 8bit for2 rd 10000 2bit for rd for2 rd def rd step
81. x y z km s defrd single single 1 appear 1000 500 2 1 2 appear 3 4 5 1 1000 2 500 2 500 se
82. MK 6 cutoff cutoff cutocf 3 cutoff cutof cutoff cutoff cutoff cutoff 15 A Ewald RYUDO 2 cutoff cutoff 2
83. NN MXDORTO Busing RYUDO RYUDO Busing 9 NT fi J m fo 4 184 6 022e23 1e3 1e10 a b 2 Busing nature
84. nature 6 1 6 H 9 9 U Alcos B r C DJ exp 2x10 3x10 r L exp L 2 6 9478e 21 2 30 A F r BE pair 1 1 Vibration 10 0 kcal mol 0 78 1 57 1 00 0 08 2 76 A B C D E F J m rad 6 1 7 Gauss Gauss
85. 1 E E defi h define NNBT34B 0 2 cutof 10 10 gcc Im 3 RYUDO def rd
86. RYUDO RYUDO RYUDO step xtrrd defrd atom extern 10 abc n0 extern 10 step 2 abc
87. pos rd Ver 1 20 vel rd for rd j Ver 1 20 sx Ver 1 20 es 53 tvlLrd rd thc rd
88. RYUDO RYUGA pm 13 nature 3 13 nature 14 EK LJ Busing Angell
89. 50 index val rd step fy 0 fs val rd id fk index E fy ftz fs index valrd ftx Val rd 1 step step ftx fty ftz fts
90. table pair KR 2 1 pm 0 01A 10 pm 0 1A 2 cutoff cutoff table 2 10 pm 2 cutoff table
91. val rd ba ete MSD val rd H 54 MSD 0 indexx HH 0 e 1 Bwald 2 3 4 e Ewald 2 3 4 e defrd disp m
92. MS Windows MS Windows 2000 Professional Visual C Ver 6 0 Service Pack 6 RYUDO Ver 1 21 MS Windows XP Professional Visual Studio 2008 Express RYUDO Ver 1 21 MS Windows XP Professional Windows Service for UNIX 3 5 RYUDO Ver 1 21 Windows 7 Professional 64bit Visual C 2010 Express RYUDO Ver 1 27c RYUDO Visual C Ver 6 0 Win32 Console Application File View RYUDO ryudo c main c load c save c disp c bndd c pote c defi h func h valu h pote c defi h define MSWINS define OLDTIMES 1 Ver 1 19 exe Visual C 2010 Express
93. RYUDO Se IT Solaris C time E Ver 1 19 3 NI gettaimeofday Linux kernel2 2 MS Windows defi h efine OLDTIMES 1 time
94. 0 0 0 0 7 0 7 1 0 MT i 0K
95. 256 gcc rdect c o rdect rdect end rd end1rd end1 rd o lt rd82t87 Ver 1 01 defrd Ver 0 82 Ver 0 87
96. more RYUDO 0 0 1 0 1 2 6 2 x y z 3 6 3 10000 16bit 0 9999 pos rd pos2 rd 10000 0 9999 4 pos rd 3 2 10000 30000 29999 3 2 6 10000 pos2 rd 5 8bit 8bit pos rd
97. 3 3 cutoff cotoff 2 cutoff 3 ul RYUDO RYUDO 2 RYUDO
98. 6 11 14 23 29 30 e Ewald a 1 2 a e Lmm 1 2L L mm a b c 1 6 1 4 14 11 1 4 50 14 1 4 74 23 1 5 13 29 1 5 72 2 0 027 A
99. 2 1 y 1 0pm 1 2 move 1 move 1 0 pm 0 0 1 pm 0 nmove x y z x y z pm 1 x 1 1 0pm 2 1 1pm 1 0 1pm
100. 0 RYUDO 0 K 1 rr r U H r ro H J m defLrd atom atom 1 1 1 0 0 50 0 6 m 1 50 0 m2
101. 100 x 100 x 100 A 90 car 1 BIOSYM CellSize x y 2z A CellSize IBIOSYM CellSize 10 0 10 0 10 0 car car 1 BIOSYM 3 A Shift x y z Shift BIOSYM
102. x y K Pa aa E a 8 y E m 6 7 8 set rd defird axis m cond K Pa elem au g moll km s pm fs axis
103. step step temp temp 1 K C temp 2 KJ KJ 7 3 Ver 1 26 RYUDO def rd
104. 6 4 2 CVFF Out of Plane CVFF Out of Plane E HX H x tetra 6 4 1 6 b CVFF 1 400 kcal moll CVFF kJ moll x 0 3 Ver 1 26 E H ncos x x0O E Hcos n x xO Ver 1 27
105. H New RYUDO EN 3 trio nature pair 2
106. bonded bondon d bonded bonded at bondon dat atom TRIBOSIM bondon dat RYUDO RYUDO bnd rd 1 1 bondon dat 1 00 1 ryudo bnd ryudo bnd bnd rd RYUDO
107. 2 x 15 3 trio 3 3 16 15 3 3 H
108. ff 9 gt DD 2CPU 1 2 1 2CPU 1 2 2 1 ntel CPU HT Linux 2 2CPU HT Linux CPU 4 2 CPU HT
109. E RYUDO 1 Visual C H 4 3 4 N3 RYUDO 2 3 4 1H
110. Ver 1 17 RYUDO 2 single horiz 3 x y 7 10 RYUDO 7 11
111. gt E gcc rdsrf c o rdsrf math E E rst rdsrf rst set rd end rd A z z rst rdsrf x y z 3 HH z
112. Out of Plane 4 3 1 def rd quad 1 2 4 1 3 1 3 Out of Plane Gik 1 RYUDO
113. 1 2 3 3 3 3 3 0 3 E 2
114. step 500step 1step 500step 501step 1000step Ver 1 18 RYUDO 2 defLrd RYUDO outsrc qcalc s 200 opt local prelib Iib22 dat atom
115. 0 def rd press defrd set rd defrrd H 0 0 1
116. E Morse def rd pair Morse 1 1 Morse 50 0 kcal moll 1 980 1 A 2 74 A 1 2 1 pm pm nature 3 Morse E D 1 e 7 0 Di
117. 16 Torsion 4 quad 4 3 E 3 ut of Plane F 3 E E 4 O tetra 17 16 Torsion 4 1
118. I 3 2 4 3 defrd iles 4 Ver 1 20 vel2 rd pos rd pos2 rd pos rd pos2 rd m s 1 2 5 3
119. 5 setrd end rd rst 6 2 3 Torsion 4 Out of Plane 4 CVFF SW 7 DR Linux 8 RYUDO 9 10 rdset rdend rdrho rdext rduni rdtxt rdsum rdmov rdmsp rdcar UN
120. oO tetra tetra tetra table 1 pair 2 3 trio 3 4 puad tetra 4 5 2 4 b CVFF
121. 1 4 2 4 01 12 m Ver 1 24 def rd b 2 Ver 1 25 set rd bonded Torsion 4 Torsion 4 17 run run
122. e L Lj Angell Angell n b o 3 aul E pm 1H A B a B N Busing Busing a b c d Busing c d d c d c LJ 1 23 3 45 Busing 1 67 0 08 1 20 3 44 3 MR
123. temp 1 K 2 K 3 step 4 step temp cond 100 5000 cond 1 thc rd 2 thc rd atom IT
124. LJ defrd LJ AB g o nature AB g o pair 6 1 2 Busing MXDORTO BMH NN
125. Ver 1 26 38 6 5 6 5 1 CVFF CVFF Biosim MSI Accelrys Discover 2 Morse 3 4 RYUDO
126. set rd ryudo end ryudo set step date set rd end rd defrd set rd rdend rst ryudo rst set rd cond set rd rst
127. step si mx step end rd val rd pos rd vel rd for rd tmp rd cutoff 2 cutoff 3 cutoff Ewald 3 step step x y z step x y 2 fix on 3 o
128. m dtx dty dtz dts index val rd step step dtx dty dtz db step ds dU step val rd id dtx index 1 m fx fy f fs
129. RYUDO NEW RYUDO NEW RYUDO NEW RYUDO NEW RYUDO RYUDO RYUDO 74
130. RYUDO ryudo c main c load c save c disp c bndd c defi h func h valu h pote c defi h define MSWINS define OLDTIMES 1 Ver 1 19 k exe Linux defrrd set rd RYUDO Enter Ver 1 19 RYUDO ANSI C C
131. 0 0 1 0 RYUDO ea 52 8 RYUDO RYUDO OS RYUDO Linux cnd rd RYUDO f cnd rd Ver 1 13 cnd rd end rd cnd rd Ver 1 13a RYUDO C S mM f H
132. 6 4 1 6 b Torsion 1 423 1 000 3 000 0 000 Torsion E kJ moll 36 6 4 Out of Plane 4 3 2 x RYUDO Out of Plane 1 j k 1 i j k 1 ik il x
133. RYUDO 2003 6 19 2004 5 13 Ver 0 85 2004 5 29 Ver 0 86 2004 6 8 Ver 0 87 2004 6 9 Ver 0 87 2004 8 23 Ver 0 88 2004 9 8 Ver 0 89 2004 9 21 Ver 1 00 2004 11 22 Ver 1 03 2005 1 20 Ver 1 04 2005 2 7 Ver 1 05 2005 6 4 Ver 1 06 2005 10 19 Ver 1 07 2005 12 24 Ver 1 08 2006 4 5 Ver 1 09 2006 4 8 Ver 1 10 No 20110310 2006 4 19 Ver 1 11 2006 4 19 Ver 1 12 2006 5 27 Ver 1 13 2006 9 14 Ver 1 15 2007 2 10 Ver 1 16 2007 4 16 Ver 1 17 2007 10 24 Ver 1 18 2008 1 15 Ver 1 19 2008 2 5 Ver 1 20 2008 9 14 Ver 1 21 2009 2 13 Ver 1 22 2009 4 15 Ver 1 23 2009 5 20 Ver 1 24 2009 9 18 Ver 1 25 2009 11 27 Ver 1 26 2010 10 19 Ver 1 27 1 2 Linux UNIX MS Windows 3 4 3 4 defrd
134. defrd 3 4 Ni 1 3 N N Ver 1 19 Ver 1 19 Ver 1 19a RYUDO make make ryudo
135. file05 dat defrd rdcar Ver 1 18 Accelrys Cerius2 MaterialsStudio car mdf RYUDO rst gcc rdcar c o rdcar Im math car mdf rdcar abc car abc mdf rdcar abc rst abc rst car mdf
136. K d 2 atom L H cond 0 2 00 pos rd 1 1 ON 0 OFF 1 2 3
137. 1 2 1 Angle 60 0 kcal moll 120 kJ moll 35 6 3 Torsion 4 4 3 3 RYUDO Torsion 4 6 3 1 CVFF Torsion CVFF Torsion 1 scos s n 360 quad
138. fix 1 10 periodic periodic 1 3 1 x 2 xy on 3 off 0 Ewald 3 BEwald 3 RYUDO 3
139. bat rd oo 1 1 bat rd RYUDO RYUDO bat rd bat rd 56 dt completed skipped running completed ryudo c c ryudo running
140. xtr rd Ver 1 13 m defrd extern extern set rd cond step cond endrd part m s xy z N x y z x y z m s x
141. set rd 3 b m 1 Ver 1 17a 0 1 2 3 b 012 23 3 01 m 123 2 n a 3 RYUDO
142. 9 tps rd pos rd tps rd 3 pos rd pos rd 4 axis 2 092267385352669e 09 2 081747525474444e 09 1 392681656459950e 09 1 0 2 0 374282511679340 0 050091092422330 0 758921370698567 1 0 2 0 125914771712974 0 948095661608534 0 258614294663550 1 0 2 0 624992622099729 0 549524764418257 0 238933083162002 2 Si 2 0 420209015130551 0 056679868129164 0 665440308805454 2 Si 2 0 079637341568431 0 942979639945443 0 165512978234313 2 Si 2 0 580156552893353 0 556768906929942 0 333552217372585 3 AIl 3 0 311948823415684 0 326293497674753 0 180830886822238 ld 0 49606402
143. MS Windows MS DOS set rd step x y z x a h p S date defLrd files 1 0
144. b c C D 1 A RYUDO pair Angell 1 1 Angell 1 0 0 16 A 3 4 A Angell 0 16 A 0 78 0 98 Aij btbj o oi Ci Di pm pm pm pm kJ moll pm kJ moll Pauling A 4 7 7 7 z n 3 Ciji Dij 3 EiE 4 5 7 ro au E 1 N RYUDO
145. co log rd RYUDO scr rd KR RYUDO Hgrd RYUDO 3 O D
146. mdf rst car P1 car car 90 rst rst RYUDO 90 rdset rdrho 90 70 car H PBC OFF car
147. set rd rdtxt pos txt vel txt for txt tmp txt 1 1 x y z hbc txt tmp txt 1 end pos txt velltxt m s for txt pN tmp txt K 3 5 defrd file
148. 72 RYUDO RYUGA MD GUI RYUDO RYUDO RYUGA RYUGA RYUGA RYUKI GUI rst 3 H uh RYUKI 73 RYUDO RYUDO RYUDO RYUDO
149. MD 4 2 6 N MI 1 1 2 1 3 2 4 3 2 1 3 12 index 2
150. OY ES RYUDO 1 1 Water 1 Water D 82 E 17 F 42 F 5 49305 1 A 0 1 A2 E 3 4 A F 3 1 H H 2 H O 3 O O 6 1 10 Coulomb 2 i d Tj RYUDO Ewald 2 cutoff
151. 5000 step 5000 3 3 3 E step 15000 step 5000 2 E 1 F set rd 3
152. RYUDO Ver 1 16 RYUDO set rd set rd E H set rd Ver 1 16a RYUDO a defrd option appear2 option option appear appear 2
153. rst P1 car rst 1 100 100 w 90 2 car 1 rst 32 qdefine ELEMS 1 9 90 90 2
154. Zap 1 3 cutoff cutoff E cutoff 500 pm 32 2 i 7 Ewald
155. 1 2 SN TT EB Dexp D s 1 K RYUDO pair 1 1 Gauss 10 0 kcal moll 2 80 A 1 00 0 50 A Gauss D s K 1 U pm pm Gauss 3 Gauss2 Gauss3 Gauss 3 4 5
156. outsrc H outsrc end rd end rd end rd osr rd step RYUDO osr rd RYUDO step 1step outsrc 51 end rd
157. 7 13 Ver 1 11 RYUDO val rd Gndex MSD index x y z val rd step step 2 16 val rd def rd file idval idv
158. atom 7 T M MT 1 appear 6 7 step 3 H atom i single 5 appear 1000 6 appear 1000 5 500 2 M 500 2 MT 10000 6 10000step atom
159. iq ftx index 1 N 1 step dU 2 100 3 4 1001step 1500step 7 14 RYUDO 1 val rd 500step 500 RYUDO E index 100 100 val rd 500step 500 step 500step 1000step 1500step
160. val rd valLrd H H val rd 2 3 id msd Gndexy MSD val rd MSD G end 1 val rd fes 2 index 3 d set rd dx 7 13 id msd H set rd part 2 1 K Pa l a index step MSD mc msd mm msd 2
161. pair nature 1 16 00 2 000 Busing 1 6 A 0 080 A Busing 1 a 2 b pm pair 00 Busing Busing nature pair 1 1 Busing 3 344 A 0 160 A
162. rdset Ver 1 00 RYUDO 19 strcture rst xtaldata 1H P1 7 xtaldata 1 rst rst xtal mdy xtal mdy xtal mdy K 300 0 end rd set rd 66 12 set rd
163. fg rd axs rd pos rd xtrrd RYUDO MXDORTO Title amo Si surface at 300K End 1000 Now 0 200 sec step Estimated finish at 6 7 13 55 55 2m22s later MSD A 2 Si 0 026 Mo 0 018 step T K P GPa UK density NN 0 Dy hr mn sc 41 787 7 0 600 1626 0 000 26 2 70 000 7 13 52 43 42 782 6 1 388 162638 80 0 000 26 200 23 860 70 000 7 13 52 43 43 796 5 1 679 162547 39 0 000 26 200 23 560 70 000 7 13 52 43 44 835 5 1 512 162366 09 0 000 26 200 23 560 70 000 7 13 52 43 45 857 4 0 955 162582 94 0 000 26 200 23 560 70 000 7 13 52 44 46 836 6 0 087 162726 93 0 000 26 200 23 560 70 000 7 13 52 44 47 827 5 0 077 162656 99 0 000 26 200 23 560 70 000 7 13 52 44 48 808 4 0 356 162731 38 0 000 26 200 23 560 70 000 7 13 52 44 49 791 0 0 788 162651 6
164. ewald NS 2 2 N cutoff j 2 Coulomb RYUDO Ewald 3 off 1 2 Ewald 10 3 4 N 3 cutoff
165. pair Coulomb 11 atom 12 RYUDO MD 2 3 eos 1 2
166. 4 oo E pos rd pos rd 1 2 7 8 7 9 59 Rl 2 Ver 1 10 id temp id msd el temp e msd Ver 1 11 el id 3 Ver 1 10 id temp val rd Ver 1 11 4 MSD Ver 1 21
167. 6 6 6 0 1 2 3 6 3 5 4 6 3 4 5 6 NR v 3 4 4 3 0 1 3 4 1 single single 1 press 0 0 GPa 0 0 GPa 1 0 GPa 1 atom 4 2 press 3 x 4 y 5 z z
168. Ver 1 07 4 24 9 6 RYUDO RYUDO 6 1 RYUDO 2 6 1 1 Lennard Jone
169. ryudo bnd bondon dat set rd bo nded bondon dat bnd rd set rd part 10000 1 10000 1 1 Ver 1 20i bonded RYUDO set rd
170. 3 4 1 4 4 oo 3 11 atom set rd 0 0
171. IBIOSYM NameMolecule end 1 car EndMolecule 0 1 1 IMoleculeFrom1 car rst elem 4 FF Type 1 FF Type 1 1 FF Type Cerius2 MaterialsStudio FF Type rdca
172. set rd end rd ad appear option appear3 appear4 io 4 amp E 7 8 46 RYUDO def rd single single
173. xtr rd xtr pre 3 xtrrd xtr pre xtr pre xtr rd xtr pre RYUDO set rd xtr rd set rd 0step RYUDO 1step 1 0step set rd rdset set rd
174. atom 1 1 1 0 0 0 2 2 2 0 0 0 H 3 3 3 0 0 0 L 2 3 1 2 3 cond cond 100 5000 z 0 1 0 3 0 7 0 9 cond 1 2 3 x y z RM 4 atom H L step step
175. 120 2 109 5 3 104 5 4 90 2 n x yw cos c n c 100 x y 90 n Qr
176. NT rdext Ver 1 03 67 RYUDO rst x y 2 CVFF Ver 1 02 y z 3 H gcc rdext c o rdext math E rdext rst x E E
177. Shift 10 0 30 0 40 0 rst car 1 FF TVpe 7 8 car B10SYM FFTypeElement StatusElement 1 8 FF Type 7 SubFFType rst FF Type rst 2 0 car 5 6 car
178. 1 step val rd 1 step val rd RYUDO RY k UDO con rd end rd H HH H 10 step MSD val rd
179. RYUDO end rd setrd RYUDO 0step xtrrd Ver 1 12b xtr rd end rd end rd 49 xtrrd end rd Ver 1 10 Ver 1 18g 1 18f
180. 2 tfr rd E tps rd axis end tvl rd def rd text 2 Im s for rd 62 for rd 32768 32877 pN tps rd axis thc rd defrd cond
181. 2 3 4 0 0 0 2 1 2 2
182. 25 3 E 100A E j A 3 3 E E 25 0 25 68 rdtxt Ver 1 03 RYUDO pos rd vel rd for rd tmp rd gcc rdtxt c o rdtxt math
183. 4 Coulomb L RYUDO CVFF 6 5 2 SW SW 2 3 lt RYUDO pair trio 6 5 3 f
184. def rd 50 RYUDO RYUDO scr rd RYUDO cnd rd end rd Val rd DOS rd pos2 rd vel rd vel2 rd for rd for2 rd tmp rd log rd scr rd tps rd ph 4
185. BIOS HT OFF Ver 1 22 Ver 1 21 bat rd end end bat rd cnd rd cnd rd log rd bat rd 37 9 RYUDO cnd rd RYUDO set rd defrd 3 1 MSD
186. force force 1 0e 9 N q force single force Ms 3 1 0e 9 N 0 0 N 1 1 Ver 1 26 E end rd pos rd wl 0 0 N 0 0 N atom set rd N y N z
187. text rdtxt 2 RYUGA rdsum Ver 1 01 RYUDO gcc rdsum c o rdsum Im math
188. 1 1 255 1 2 _ 3 E 2 2 A RYUDO 0 5 A ua u
189. cond 80 80 part 80 set rd set rd step ryudo c gcc rdend c o rdend math end rd
190. rdend set rd x rdend x drho Ver 1 03a 2 90 3 90 RYUDO 90 Ver 1 03 gcc rdrho c o rdrho Im math rdrho
191. RYUDO RYUDO RYUDO 1 s Pa atm m AI J cal l mol l K C mbar step au eV
192. 8 toff 3 4 8 HI gt 4 RYUDO E 253 E 3 4 3 0 cutoff 3 4 cutoff 3 300 500 pm cutoff
193. 5 Verti z 0 2 vpot dat 1 2 verti 3 G y 4 5 Numeric ET m 7 9 Ver 1 18 2 MD RYUDO 2
194. NameMolecule mdf rst bond RYUDO setrd Ver 1 21 65535 65535 1 rdcar 65535 rst RYUDO rdset RYUGA rdcar 3 E car 8 rst elem 4 0 0 rdset 71 rdcar c
195. RYUDO 2 atom single atom 4 atom oo R CO MM oo 0O MM oo R 0O 0 0 1 0
196. 1 0 GPal RYUDO 1 44 2 3 4 5 6 7
197. MSD set rd 1 0 1 MSD id msd 2 mc msd mm msd MSD defrd set rd m2 0 1 2 MSD set rd 0 1 4
198. mc msd mm msd 3 0 1 4 MSD defi h defne MOLESD 3 mce msd mm msd mc msd 1 mm msd 2 0 5 Ver 1 22d 0 000 pos rd defird ies 3 Ver 1 20 pos2 rd
199. RYUDO 3 6 1 9 2 2 6 2 3 2 Bunsing Morse 3 6 2 3 2 3 CVFF
200. defrd Ver 0 82 RYUDO Ver 0 82 0 86 RYUDO defrd RYUDO Ver 0 86 0 87 defrd Ver 0 86 bonded defrd 0 82 0 87 def rd ryudo def 0 87 Ver 0 87 gcc rd82t87 c o rd82t87 math def rd rd82t87 rd82t87 gt def new Ver 0 82 Ver 0
201. end rd end rd 0 pos rd val rd end rd end rd val rd more val rd cnd rd pos rd flg rd axs rd
202. RYUDO b 2 4 2 b set rd bond set rd defird bonded
203. pos2 rd 6 8bit 1 1 8bit 4 0 0 1 0 0 10000 pos rd pos2 rd MSD 1 16bit 3 2 pos2 rd 10000 pos2 rd 10000 6 3 pos2 rd 6 10000 pos rd 30000 19 60 1x6
204. 3 si pm J mx A kJ mol 0 5 files RYUDO end rd val rd MSD pos rd vel rd for rd tmp rd
205. 7 Ver 1 26m RYUDO atom Ver 1 15 RYUDO W 1 E OK
206. erg e A A 006 IE lu m c k M G 18 Im 3 kcal moll RYUDO disp 2 Out of Plane 4
207. 100 1000 10000 FF Types 64 define ELEMS MOLES ATOMS FF Types FFTTS MaterialsStudio car mdf rdect Ver RYUDO Ver 1 10a 1 12b end rd 3 RYUDO endrd Is 1 256 rdect end rd RN end1 rd
208. LJ 1 1 Lje 0 050e 20 274 0 1 2 o pm LJ nature g o pair nature g c m gi g 2 LJe eee 26 T 07 9 2 Kong RYUDO LJk 1 13 ee 2 EO 7 Le Ei EEO LJe LJk nature pair
209. end axis 475 33e 12 824 00e 12 separate 4 8 0 3 9531284599999998e 19 0 4 6458793400000003e 19 0 3 9762739000000000e 19 0 3 8056311400000000e 19 CS TO 3 7651346299999999e 19 3 7541889800000002e 19 1 2 3 4 2841242500000001e 19 end e x 2 e y x 47 z x y axis
210. 3 3 pos2 rd 21 14 14 2 Ver 1 19 RYUDO pos2 rd 30000 20000 30000 20000 pos rd pos2 rd def rd step vel rd 30000 30000 6 pos rd 36 21
211. n0 xtr rd set rd part xy 1 fopen 2 set rd xtr rd
212. 0 3728000 0 1272000 0 3095000 0 1905000 8 1 SYNTHETIC ZEOLITE 2 0070e 09 300 0 1 9920e 09 100000 16 00 28 09 26 98 3 4 0 0665000 0 9335000 0 5665000 0 4335000 0 9335000 0 0665000 0 4335000 0 5665000 0 0621000 0 9379000 100000 0 7603000 0 1920509 0 0432682 0 0765181 7 0 2603000 0 0777483 0 1520491 0 2397000 0 1965809 0 2040482 0 1833487 0 7397000 0 0028992 0 2375698 0 2019596 0 2397000 0 2412319 0 0958395 0 1505995 0 7397000 0 0479984 0 0899982 0 1563883 0 7603000 0 2492714 0 0195789 0 0475502 0 2603000 0 0348806 0 0959110 0 1968718 0 9239000 0 0378799 0 0418711 0 1733494 0 4239000 0 0595903 0 1054811 0 1130104 100000 5 5 6 6 7 2 1 3420e 09 90 000 90 000 90 000 3 100000 4 0 1410484 2 3 4 5 5 6 3 72 E x y 1 Ju A 0 70 RIRRYSS 00
213. 4 63 E 1 1 X x pos rd 6 1 5 6 7 bondon dat bnd rd 8 axs rd Ver 1 09 pos rd pos rd x y z 1 step more Excel val rd
214. BB Se nature 15 nature 0 1 0 1 10 0 nature LJ Busing Angell 1 2 Busing 2 800 A 0 160 A 1 2 Morse 12 0 kcal mol 1 980 1 A 2 880 A 1 2 Busing M
215. end rd 1 rdset rdset set rd set rd RYUDO cartesian Ver 1 08 Ver 1 19 detrd b RYUDO 2 2 RYUDO 4
216. 0 1 8 2 0951 A z A kJ moll B p q a c pm trio 1 11 SW 72 9 J 1 2 1 8 2 0951 A g kJ moll al c pm 6 2 3 34 HzO 3 2 Up D 1 cos 2 0 0 6 ki k j
217. 50 defrd Ver 0 50 defrd RYUDOVer 0 50 Ver 0 81 msport bonded Ver 0 82 rd82t87 ryudo def 0 50 ryudo def 0 82 def rd Ver 0 51 0 81 0 50 Ver 0 49 Ver 0 49 defrd defrd
218. Morse 120 0 kcal mol 2 000 1 A 1 340 A 12b Morse 116 0 kcal mol 1 770 1 A 1 080 A trio 15 343 SW 15 111b Angle 90 00 kcal mol 120 00 211bAngle 37 00 kcal mol 120 00 quad 16 1111bTorsion 12 000 kcal mol 1 00 2 00 180 000 6 2111bTorsion 12 000 kcal mol 1 00 2 00 180 000 2112bTorsion 12 000 kcal mol 1 00 2 00 180 000 run 17 1 def rd 2 72 3 4 5 6 7 8 9 10 11 1 12 19 19 14 14 15 5 16 16 17 A t 1
219. RYUDO 2 x y z 3 5 3 m s vel2 rd 10000 16bit vel rd H 32768 32767m s Am 0 9999 16bit 4 16bit 8bit 8bit vel rd vel2 rd 5 8bit 1 1 vel2 rd 10000 2bit velrd vel2 rd def rd step for rd def rd Ver 1 20 pos rd pos2 rd for2 rd H 8bit
220. b c d nature 1 16 00 2 000 Busing 1 6 A 0 080 A 49 09 1 20 kJ 5pm mo195 kJ pm mol05 pair 1 1 Busing 3 344 A 0 160 A 2498 0 1 82 kJ pm6 moll kJ pm moll 28 6 1 3 Angell BMH Busing 2 4 exp 2 C Di Pj 7 Busing m fb 4 184 6 022e23 1e3 1e10 A Pauling ON
221. 0 0 90 0 temper 691 8531408 682 6863706 0 0000000 press 8 09419302e 08 7 92745426e 08 8 40264746e 08 7 95247735e 08 0 0 0 energy 0 00000000e 00 0 00000000e 00 2 08610142e 16 1 23938831e 17 axis temper press density 0 00000000e 00 id temp 6 8082996606e 02 2 2866198585e 03 id msd 5 5139805481e 21 1 2047791783e 20 end m RYUDO 90 K val rd 3 0 x y z o 8 y 0 energy Ewald 3 4 2 J density kg m3 5 id temp Gndexy step
222. 9 0 000 26 200 23 560 70 000 7 13 52 44 50 818 6 1 311 162437 28 0 000 26 200 23 560 70 000 7 13 52 44 Title amo Si surface at 300K End 1000 Now 0 100 sec step Estimated finish at 6 7 13 54 19 2m19s Iater MSD A 2 Si 0 031 Mo 0 017 End 1000 Total 865 Defect 0 Atom 2 Nature 2 Index 2 PressX 0 11821 PressY 2 32064 PressZ 1 49444 GPa EnergyK 8830 70 C 0 00 S 171267 99 total 162437 28 kJ mol Index Name Number Temparture K MSD A 2 Si 864 814 593596 0 030580 Mo 1 462 248781 0 017493 step T K P GPa U kJ mol density axis x y z A Dy hr mn sc 51 838 2 2 008 162504 18 0 000 26 200 23 560 70 000 7 13 52 45 52 817 2 1 912 162810 00 0 000 26 200 23 560 70 000 7 13 52 45 53 769 9 1 440 162801 61 0 000 26 200 23 560 70 000 7 13 52 45 54 798 7 0 316 162362 94 0 000 26 200 23 560 70 000 7 13 52 45 55 823 7 0 109 162543 39 0 000 26 200 23 560 70 000 7 13 52 45 56 793 7 0 182 162767 59 0 000 26 200 23 560 70 000 7 13 52 45 1 defrd disp 1 2 3 1 g c
223. 9308648 0 496622787387862 0 002929194691235 en akis m 1 No x y z defrd text 1 tyl rd vel rd ve rd 32768 32877 m s tps rd axis trd end for rd NT vel rd
224. Busing 1 a 2 b pm atai bi b 1 6 A 0 08 A 3 2 A 0 16 A RYUDO Busing a a r Cc c d d E fo b b exp c d a b c d c d nature pair a
225. al dts fx idval file TAB fle fle idval dx dy dz ds index val rd step dx dy dz 0 dt step ds d0 step valrd id dx index 1
226. ff 1 2 3 1 2 3 set rd atom atom 1 2 parr pair 2 table 2
227. j ik 17texplg 7oy 0 1 trio 1 2 1 Water 1 1e 11 99 5 7 0 1 A 1 40 A 7 0 1 A 1 40 A kJ moll gi 1 pm rilpm gk 1 pm rmklpm 6 2 4 CVFF 3 Angle CVFF Unit cutoff ON OFF 9 6 H 9 trio
228. m3 ndexy MSD T 1 f xyz Ewald 3 Gndex gt y MSD YS4t disp 4 ndex MSD HH H val rd
229. orse Ewald b n Ver 1 17a m 0 a
230. pos2 rd pos rd Ver 1 19 3 0 2 0 3 0 2 0 64 HH defi h define HH 65 10 RYUDO rd rdset Ver 1 36b set rd rdset c math gcc rdset c o rdset Im rst
231. r FF Type SubFFType 2 rst bond FFTypeElement BondFileOutput car bnd bnd rd F1 3 RYUDO defrrd bonded rst 0 rst bond BondFileOutput
232. rio 1 3 2 24 2 E E Ver 1 17a b 1 defrd b 2 Ver 1 25 12 m 1 2 SW
233. s AB A BB r RYUDO 1 1 LJ 123 23 32 23 LJ 1 A 2 B pair LJ kcalAl2 moll kcalA6 moll nature LJ pair nature ml B jm A B 2 4 Y4 4 Bi VB B LJ E o g c ee RYUDO
234. set rd osr rd 1 1 1 4 x y z 1 254 0 233 1 9872e 8 2 3467e 9 7 0098e 9 0 0 1 0 0 0 RYUDO 100 1 0 100 1e 10 RYUDO 0 9999999999 1e 10 0 999999999 N e osr rd osr rd
235. set rd part cond xt1 xtaldata 1 1 car xtt xtal mdy Colors rst 4 Oo rdset set rd rdend rdset strcture rst RYUDO xtal mdy 2 HH xtl 300 0 rst Fl de
236. step 10 9 press RYUDO x y z Pa atm bar mHg Pa
237. t rd 3 HH 4 O 3 0 0 ad 0 000 0 000 0 900 0 000 0 000 1 000 3 0 0 ad 0 100 0 000 0 900 0 000 0 000 1 000 400 ad 0 050 0 000 0 850 0 000 0 000 1 000 defrd 3 H 4 O single 3 appear 1000 500 2 4 appear 1000 500 1 45 E lt B E
238. x atom 1 1 0 e 7 1 7 8 7 9 Ver 1 22d 0 000 RYUDO Error Too high temperature 1
239. y z N date end rd ryudo xtr 1 00 title sample aXis 1 107800000000000e 08 5 000000000000000e 09 2 960000000000000e 09 90 0 90 0 90 0 cond MIE 2388751390 Pa 3583873590 Pa 59885444 Pa 3570441669 Pa step elem No Name Weight au cl 12 0100000 2 c2 12 0100000 3 c3 12 0100000 part 1 0 0 b 0 696544718316033 0 567156442248992 0 511624201476373 1 127611769590422e 03 1 ON 6 871310355572089e 02 2 333598199034652e 09 1 289848326161689e 10 7 358118422 e 1 0 0 b 0 705417452222422 0 608266672012285 0 523230579417609 7 084618170613594e 02 1 136979243246304e 02 1 098169315337051e 02 2 371887179944112e 09 8 789512224408459e 10 7 8142739 61653595e 10 date 04 36 19 05 27 pos2 rd vel2 rd for2 rd H EXTPVFOUT 0 pos2 rd
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