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. part 1 1 Numeric flename f ename TD 1 1 m 6 1 9
6. atom single atom atom 42 3 3 3 0 0 4 4 4 1 0 0 5 5 5 0 0 0 X 6 6 6 0 0 0 X 1 2 3 6 3 5
7. atom 7 appear 6 T M MT
8. MK 6 cutoff cutoff cutocf 3 cutoff cutof cutoff cutoff cutoff cutoff 15 A Ewald
9. set rd 0 0 0 0 0
10. 53 AAA 5000 step 10000 step 5000 ryu 3 les disp ewald ewald temp 3 press 2 2 J
11. atom OK ea il PE EE ot 1 12 4 4 1 2 MgO FezO MD 3 0 0 0 4 2
12. RYUDO RYUDO 1 s Pa atm m A cal l mol l K C mbar step au
13. Ver 1 16 RYUDO OK RYUDO set rd Ver 1 16a RYUDO a amp set rd set rd defrd option appear2 option option
14. tps rd pos rd pos rd 59 tps rd 3 H pos rd 4 H axis 1 0 2 1 0 2 1 0 2 SI 2 2 2 3 a n co oP 2 092267385352669e 09 2 081747525474444e 09 1 392681656459950e 09 0 374282511679340 0 125914771
15. Ver 1 10 velrd twl rd move move Ver 1 11 move 7 6 RYUDO 2
16. Ver 1 17 RYUDO 3 x y z single horiz 7 10 46
17. or or S or Too short 0 1A Too short
18. 13 137 nature au e pm LJ Busing Angell L LJ 14 A
19. 10 100 3 defrd step 1 ryudo c set rd 56 ryudo c Val rd
20. RYUDO gettaimeofday Linux kernel2 2 MS Windows Visual CH defi h define OLDTIMES 1 time Ver 1 19 3 4 NI 3 4 N3
21. 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 3
22. defrd Ver 0 82 RYUDO Ver 0 82 0 86 RYUDO def rd RYUDO Ver 0 86 0 87 defrd Ver 0 86 bonded defrd 68 0 82 0 87 defrd ryudo def 0 87 Ver 0 87 gcc rd82t87 c o rd82t87 math
23. 1 MD RYUDO MD MD RYUDO
24. x y z Pa fix 1 10 periodic periodic Pa atm bar mHg 1 1 3 1 x 2 xy on
25. 1 2 1 3 1 4 1 2 3 _ Torsion k J 1 Out of Plane Gik 1 3 RYUDO RYUDO pair 2
26. RYUDO NEW RYUDO NEW RYUDO RYUDO NEW RYUDO RYUDO NEW RYUDO R
27. RYUDO RYUGA MD GUI RYUDO RYUDO RYUGA RYUGA RYUGA RYUKI GU rst RYUKI 69 RYUDO RYUDO RYUDO
28. MS Windows cnd rd Enter Ver 1 19 RYUDO ANSI C C RYUDO
29. RYUDO Solaris RYUDO RYUDO C time
30. 2 0 3 b Im o a 2z2 1 Ver 1 17a 01 12 m 2 b 0 4 1 4 2 4 2 b
31. ryujim d3 dion ne jp miura aki che tohoku ac jp RYUDO RYUDO NEW RYUDO RYUDO RYUDO rdset
32. 3 4 N 3 cutoff 3 4 N N Ewald Ewald Es gt periodic Ewald 1
33. step OS RYUDO 32bit Linux 2GB 64bit Linux 2GB 7 12 Ver 1 10 Ver 1 18h tps rd pos rd 10 RYUDO i MSD
34. E E b RYUDO RYUDO set rd bond nded def rd bo bonded bonded bondon dat atom TRIBOSIM bondon dat RYUDO bnd rd 1 bondon dat
35. def rd single force single 1 force 1 0e 9 N 0 0 N 0 0 N single force single E force atom set rd force x N y N z N N 1 x 1 0x10 N Ver 1 06 force 1 forc
36. 1 RYUDO 1 RYUDO RYUDO step xtr rd defrd atom extern 10 abc n0 extern 10 step De
37. 1 ryudo def RYUDO def rd def rd RYUDO RYUDO def rd def rd RYUDO 2 title def rd title 72
38. 4 24 9 6 RYUDO RYUDO 6 1 RYUDO 2 6 1 1 Lennard Jones
39. pos rd Ver 1 20 vel rd for rd j Ver 1 20 sx Ver 1 20 es 51 tvlrd tfr rd thc rd knd rd No
40. 6 1 6 4 cos g7 C exp 2x10 3x10 exp E F 7 L 2 6 9478e 21 A F r 2 pair 1 1 Vibration 10 0 kcal moll 0 78 1 57 1 00 0 08 2 76 A B C D E F m rad 6 1 7 Gauss Gauss 1 2
41. 1 E R 6 1 val rd 16 RYUDO SR 13 E nature
42. 3 RYUDO B E pair a 2 3 01 012 0123 1 12 123 2 EX Sr gt o 2 o m 4 set rd m
43. set rd step ryudo c gcc rdend c o rdend math end rd rdend set rd x rdend x drho Ver 1 03a
44. N E E 3 E ks 4 E E def rd atom 7 M def rd step 20 3 0
45. b m 0 a 2 3 m b 1 Ver 1 17a 0 3 1 3 2 2 01 2 b b
46. 0 4 0 3 e end lt axis 475 33e 12 824 00e 12 SeDarate 4 8 0 3 9531284599999998e 19 0 4 6458793400000003e 19 0 3 9762739000000000e 19 0 3 8056311400000000e 19 Ch SO 1 7 3 7651346299999999e 19 2 7 3 7541889800000002e 19 7 4 2841242500000001e 19 en e x z e y z x e z x axis
47. 1step H RYUDO E 1 E
48. dD step valrd id dx index 1 m dtx dty dtz dts index val rd step step dtx dty dtz db step ds dU step val rd id dtx index
49. E Ewald b n Ver 1 17a m 09 a b m set rd 3 1
50. Warning nn table over flow 3 3 cutoff cotoff 2 cutoff 3 RYUDO RYUDO 2 RYUDO
51. 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 A N e osr rd
52. rd rdset Ver 1 36b set rd rdset c math gcc rdset c o rdset Im rst set rd part cond xt1 xtaldata 1 1 car xtt xtal mdy Colors rst 4 Oo rdset
53. math gcc rdmsp c o rdmsp math fle05 dat bondon dat rdmsp defrd bndrd 3 66 E bnd rd RYUDO bondon dat ryudo bnd 0 87 1 1 1 2 Ver 0 87 RYUDO bondon dat bonded
54. density 0 00000000e 00 id temp 6 8082996606e 02 2 2866198585e 0 id msd 5 5139805481e 21 1 2047791783e 2 end 3 0 2 62000000e 09 2 35600000e 09 7 00000000e 09 90 0 90 0 90 0 0 0000000 8 09419302e 08 7 92745426e 08 8 40264746e 08 7 95247735e 08 0 0 0 axis temper 691 8531408 682 6863706 press energy 0 00000000e 00 0 00000000e 00 2 08610142e 16 1 23938831e 17 axis m RYUDO 90 temper K val rd 3 0 y z c Pal a press 0 energy Ewald 3 4 density kg m3
55. defird AB g o nature AB g oc parr 6 1 2 Busing MXDORTO BMH RS
56. set rd 43 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 x y z km s defrrd single single 1 appear 1000 500 2 1 2 Iappear
57. b m b b trio gt 3 3 1 16 m o
58. x y x y 2 km s 8 H RYUDO 90 00 90 00 90 00 cond def rd temp 2 set rd part
59. 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 kJ moll pm pm 6 2 2 SW
60. 3 2 30000 4 20000 30000 3 20000 pos rd pos2 rd def rd step vel rd defrd iles 4 Ver 1 20 vel2 rd
61. 29 oy SR k cutoff gi m Di UFF Bi 0 5 ki D 0 RYUDO pair 1 1 Harmonic 140 0 kcal moll 1 0 kJ m 2moll 2 70 A CR Di Bi TI kJ moll kJ mimoll pm nature
62. atom IT 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
63. 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 0 3728000 0 1272000 0 3095000 0 1905000 8 1 SYNTHETIC ZEOLITE
64. Se Se A 2 7 nature f E 2 Fg Le nature 0 Hi
65. g cm 0 1 ndexy MSD xyz Ewald 3 index gt y MSD disp 4 Gndex MSD val rd MSD 0
66. e defird disp mx atom 1 1 0 e 7 1 7 8 7 9 RYUDO Error Too high temperature 1
67. def rd pair Morse 1 Morse 1 1 Morse 50 0 kcal mol 1 980 1 A 2 74 A 3 1 2 1 pm pm E nature J Morse 7T H E 7 7 0 Dj
68. 7 0 7 1 0 MT
69. y z rdsum filename elementNo x y z filename pos rd velrd for rd tps rd tvl rd tps rd elementNo set rd elem x y z 1 kndrd valrd 1 1 V
70. make ryudo bin gcc UNIX RYUDO ANSI cc makefile GCC gcc CC cc 0PT c ansi Wall make MS Windows Ver 1 21
71. set rd rdend rdset strcture rst RYUDO xtal mdy 2 HH xtl 300 0 rst Fl de rdset Ver 1 00 RYUDO 19 strcture rst xtaldata 1H P1 7 xtaldata 1
72. 1 b 19 CVFF Morse A 4 CVFF gle 3 b RYUDO Js b 2 4 2
73. 2 3 RYUDO Ui 2 Us 3 4 et x x Xj dA 2 Ck tS Xd 3 x o x r o xxx rk o Ui 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 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
74. Ver d 2 3 atom L H cond 0 88 knd rd RYUDO gl 1 1 2 3 X2 pos rd 3 1 set rd 1 1 DO OO tM 8 axs rd Ver 1 09 pos rd x y z
75. val rd cnd rd pos rd knd rd axs rd 100 1000 10 000step 10 100
76. E H n cos x Xo H n x x 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 _ 6 4 2 CVFF Out of Plane CVFF Out of Plane E HX H x tetra
77. part 4 d a 0 23 gt bond bondon dat end rd end rd set rd set rd
78. 7 step atom single 5 appear 1000 500 2 M 44 6 appear 1000 5 v 500 2 MT 10000 6 10000step atom 7 Ver 1 15 RYUDO atom
79. 1 H H 2 Eexp F r G H O 3 O O 6 1 10 Coulomb 2 4 04 RYUDO Ewald 2 cutoff RYUDO Ewald 3
80. rst rst xtal mdy xtal mdy xtal mdy K 300 0 end rd set rd 63 12 set rd end car xt set rd Structure0 31 elem E set rd def rd rst TRI
81. 2 3 step MD 1 0 1 RYUDO 1 fs 10 5 1 3
82. e 4 MSD Ver 1 21 MSD set rd 1 0 1 id msd 2 mp e msd Ver 1 11 MSD mc msd P Fa mm msd O 57 MSD
83. Ei 2 J F K K E 0 id temp Gndex gt index step step val rd val rd valrd 2 3 id msd Gndexy MSD val rd MSD index 3 set rd end 1 valrd fes 2 d dx 7 13 id msd 1
84. gcc rdext c o rdext math E 1 rst gcc rduni c o rduni math rduni rst 1 rst 2 2 Y bond 3
85. val rd id ftx index 1 N step dt 2 index 100 100 100 3 val rd 500step 500step 500step 1000step 1500step 49 4 val rd 500step 500step 1step 500step 501step 1000step 1001step 1500step
86. amp 0 Ewald 1 step
87. def rd single 5 Verti z 0 2 vpot dat 1 2 verti 3 x y 4 eS Numeric mm J 7 9 Ver 1 18 I 2
88. RYUDO 0 5 A ua u 1 temp cr press or RYUDO
89. RYUDO RYUDO RYUDO RYUDO PR 2
90. ryudo end ryudo set step date set rd end rd defrd set rd rdend rst ryudo rst set rd cond set rd rst end rd
91. MS Windows 2000 Professional Visual C Ver 6 0 Service Pack 6 MS Windows XP Professional Visual Studio 2008 Express MS Windows XP Professional Windows Service for UNIX 3 5 Visual C Visulas Studio Win32 Console Application File View RYUDO c h pote c defi h define MSWINS define OLDTIMES 1 Ver 1 19 Gk exe Linux defLrd set rd
92. b 2 trio b 1 m 12 2 0 E b E E 3 a a m o
93. N3 N Ver 1 19 defi h define NNBT34B 0 9 Ver 1 19 2 cutoff Ver 1 19a RYUDO 10 Imake make ryudo 10
94. RYUDO outsrc qcalc s 200 opt ocal prelib lib22 dat outsrc end rd step end rd end rd osr rd RYUDO osr rd RYUDO step 1step outsrc end rd set rd
95. axs rd pos rd xtrrd lt 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 3
96. MD 2 3 ce 1 2 ve 3 4 1 4 4 11 atom
97. KM RYUDO 2 3 4 1 defird 3 4 N 1
98. a quad b a m o 2 2 012 01 12 1 Torsion 4 Torsion 4 17 run run RYUDO
99. for rd def rd iles 5 Ver 1 20 for2 rd pos rd pos2 rd pos _rd pos2 rd RYUDO N 1 2 5 2 x y 3 5 3 pN 16bit for rd 32768 32767pN for2 rd 10000 0 9999 16bit 4 16bit 8bit 8bit or rd for2 rd 5 8bit 1 1 8bit for2 rd
100. 3 FL Index 12 MSD 12 index
101. atom H L step step step step temp temp 1 K C temp 2
102. mol gt1 pm rilpm gl1 pm rlpm 6 2 4 CVFF 3 Angle CVFF Unit cutoff ON OFF 9 6 H 9 trio 1 2 1 Angle 60 0 kcal moll 120 kJ moll
103. 1 rst 32 qdefine ELEMS 1 9 90 90 2 120 2 109 5 3 104 5 4 90
104. 3 1 3 E postxt vel txt for txt tmp txt E 1 x y z tmptxt 1 pos txt E hbc txt H eng E vel txt m s for txt pN tmp txt K 3 5 2 65 def rd file 4 text
105. bnd rd RYUDO defrd bonded rst 0 rst bond BondFileOutput NameMolecule mdf rst bond rdcar 3 car 8 rst elem 4 0 0 rdset rdcar c 100 1000 10000
106. 6 4 1 6 b CVFF 1 400 kcal moll CVFF kJ moll x 0 36 37 6 5 6 5 1 CVFF CVFF Biosim MSI Accelrys Discover 2 Morse
107. MD RYUDO 45 2 defLrd single 5 horiz Zz 0 2 hpot dat 1 2 horiz 3 y 4 5 axis m e separate e
108. rdtxt Ver 1 03 pos rd vel rd for rd tmp rd gcc rdtxt c o rdtxt math E 64 1 1 define 7 RYUDO set rd rdtxt
109. s TT g exp D s K RYUDO pair 1 1 Gauss 10 0 kcal moll 2 80 A 1 00 0 50 A Gauss D s K 1 pm pm Gauss 3 Gauss2 Gauss3 ff 30 Qr E Gauss 3 4 5 Bi 6 1 8
110. car Em 4 FF Type 1 FF Type 1 1 FF Type Cerius2 MaterialsStudio FF Type rdcar FF Type FFTypeElement SubFFType rst bond 3 car BondFileOutput bnd
111. ewald 2 6 11 14 23 L a b c 6 1 4 14 e 1 2 w Ewald gw Q Lam 1 2 mm 3 o 1 o 1 11 1 4 50
112. pair trio 6 5 3 f RYUDO 3 6 1 9 2 2 6 2 3 2 Bunsing Morse 3
113. 2 01 12 1 2 SW E 2 012 3 RYUDO pair trio 16 Torsion 4 4 3 quad F 3 4 O tetra 16
114. n 2 3 23 E 3 3 3 3 2 4
115. 3 pos2 rd 1x6 3 3 pos rd 30000 30000 6 pos rd pos2 rd 21 14 pos2 rd 10000 pos2 rd 10000 6 6 10000 pos rd 30000 36 21 14 2 Ver 1 19 RYUDO pos2 rd
116. set rd set rd 11 set rd 0 RYUDO Sv 1 10 10step 10step
117. val rd MSD pos rd vel rd for rd tmp rd end rd end rd 0 pos rd val rd end rd end rd val rd more
118. AB A BB 2 6 4 r RYUDO pair LJ 3 1 1 LJ 123 23 32 23 LJ 1 A 2 B kcalA moll kcalA mol nature pair 4j V4 4 B B B nature Jm Jm LJ g go g c g 4 Je RYUDO LJ 1 1 Lje
119. H E ryudo c ryudo c SI MXDORTO cnd rd set rd end rd PATH
120. 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 No 20080914 2005 12 24 Ver 1 08 2006 4 5 Ver 1 09 2006 4 8 Ver 1 10 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 1 2 Linux UNIX MS Windows 3 4 3 4 defrd 5 setrd
121. gcc Im 3 RYUDO def rd set rd km s
122. tyl rd E ve tfr rd for rd tfr rd for rd 32768 32877 pN 3 1 H E rd 32768 32877 m s tps rd axis end m s defrd
123. 2 set rd xtr rd xtr rd xtr pre 3 xtrrd xtr pre xtr pre xtr rd xtrpre RYUDO setrd xtr rd set rd
124. i 1 2 Coulomb 1 00 2 00 e Coulomb 2 2 cutoff cutoff 32 6 2 RYUDO 3 6 2 1 Unit
125. 7 2 RYUDO 39 defrrd temp 1 K 2 K 3 step 4 step temp cond 100 5000 cond 1 thc rd 2 thc rd
126. 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 Ver 1 07
127. 2 1 pm 0 01A 10 pm 0 1AA 2 cutoff cutoff n b O a b c d E F pair Busing table pair a E N LJ 1 23 3 45 Busing 1 67 0 08 1 20 3 44 1H
128. 2 1 Ewald 0 0 Ewald RYUDO Coulomb Ewald Coulomb pair 0 0 Coulomb nature nature nature nature
129. 1 16 00 2 00 Angell 8 0 407 1 420 3 92 1 86 10 Angell ni b ei 1 Ni pair Aij bi bj go roj ij Djj nature E oi 3 6 1 4 Morse Morse RYUDO E D lexp 28 r r 2exp B r r D i 8 ri Morse
130. step 3 do def E 1 def rd ryudo defl 5000 step 5000 step 15000 3 run 0 periodic atom
131. abc rst car E mdf car P1 car 3 H rrst RYUDO car E 90 rst 90 rdset rdrho 90 car car 100 x 100 x 100 A 90
132. ai ai brb 1 6 A 0 08 A 3 2 A 0 16 A RYUDO Busing ic dd E fo b b exp 5 8 c d a b c d c d nature pair a b c d
133. 3 4 5 1 1000 2 500 2 500 ff set rd 3 H 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
134. 34 6 3 Torsion 4 4 3 3 RYUDO Torsion 4 6 3 1 CVFF Torsion CVFF Torsion 1 scos s n 360 quad 6 4 1 6 b Torsion 1 423 1 000 3 000 0 000 Torsion E k
135. Gndexy valLrd a 0 MSD val rd T ul 52 e 1 Ewald 2 3 4 e Ewald 2 3 4
136. indexy MSD Xy Xz 2 xyz 3 si pm J mx A kJ mol 0 5 files RYUDO end rd
137. Bb Coulomb 2 v table 10 pm 2 cutof 0 0 2 3 4 14 ON 1 2
138. 1 step val rd 1 step val rd RYUDO RY k UDO con rd end rd H HH H 10 step MSD val rd
139. pair 2 table 2 0 0 3 table G k 1 2 j 2 Torsion 4 table G k D
140. OH LJ CVFF 0 5 fs 0 1 fs 7 RYUDO detrd single single single atom index 7 1 RYUDO defLrd
141. 1 pos rd K 0 set rd def rd atom 0 pos rd H E defrd extern extern set rd cond
142. 1 bondon dat 1 ryudo bnd ryudo bnd 1 00 bnd rd 2 Ver 1 20i set rd bonden 4 H RYUDO
143. car E H PBC OFF E car 1 BIOSYM Shift x y z Shift 10 0 30 0 40 0 rst 8 car car 1 FF Type 7 TBIOSY FFTypeE lement
144. RYUDO 2 cutoff cutoff 2 1500 pmj defrd cutoff a b c NRN 3 cu HI toff
145. 1 18f 7 13 Ver 1 11 RYUDO val rd Gndex MSD index x y z val rd step EL HH step 2 16 val rd
146. MXDORTO Busing RYUDO RYUDO Busing a a r E b eT ff m fo 4 184 6 022e23 le3 1e10 a b 2 Busing nature pair
147. 0 defrd les 3 Ver 1 20 pos2 rd more 4 RYUDO E 0 0 1 0 1 2 6 2 x y z 3 6 3 10000 16bit 0 9999 pos rd pos2 r
148. HT Linux OS CPU 4 2 CPU HT BIOS HT OFF SS 9 RYUDO cnd rd RYUDO set rd defrd 3 1 MSD
149. 0 def rd press defrd set rd def rd H 0 0 1
150. 0step 1step 1 0step setrd rdset set rd RYUDO RYUDO end rd set rd RYUDO Ostep xtr rd Ver 1 12b xtrrd end rd 3 end rd xtrrd end rd Ver 1 10 Ver 1 18g
151. 2 H H H O O O H H NRN B RDG h A fo 4 184 6 022e23 1e3 A4 36 1345 A B 18 C 40 1 A D 82 E 17 F 7 62177 1 A2 G 1 45251 A H O 4 10 4 Co AN Va EPE GS fp S 72 269 A B 6 361637e 92 C 9 19912 D 40L1 A E 42 F 5 49305 1 A G 12 08471 O O 4 B _ exp D r E exp F r G pe 4 en amp A 144 538 A B 6 862097675e 85 C 8 8591 D 4 0 1 A2 E 3 4 A F 1 5 1 A2 G 4 5 A RYUDO 38 1 1 Water 1 Water
152. bat rd RYUDO RYUDO bat rd cnd rd log rd RYUDO bat rd ryudo c 2CPU 1 2 1 2CPU 1 2 2 1 2CPU
153. KJ KJ 7 3 RYUDO defird autodel z 0 8 40 autodel G x y y z z 0 99 0 def rd atuodel atom 7 4 RYUDO
154. nature 1 16 00 2 000 Busing 1 6 A 0 080 A 49 09 1 20 a kJ Ppm mol7 kJ Ppm mol05 pair 1 1 Busing 3 344 A 0 160 A 2498 0 1 82 kJ pm moll kJ pms mol 6 1 3 Angell BMH Busing 2 2 4 20 aa i i Di 5 Busing J m fb 4 184 6 022e23 1e3 1e10 A Pauling b c C D RE
155. step 1 step 20step 30step 10 step MD step step step 8 10 Ver 0 85 RYUDO
156. 6 2 3 2 3 CVFF Morse Discover NH Sh 38
157. 3 E 3 ryudo bnd bnd rd set rd defLrd bonded bnd rd bondon dat set rd part 10000 1 10000 3 E 2 1 A 9 2 7 E RYUDO
158. abc n0 xtr rd set rd part 47 xy E 1 fopen
159. 14 1 4 74 23 1 5 13 29 1 5 72 2 0 027 A 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 8 3 set rd temp E RYUDO 29 30
160. defrd file idval idval dts fx idval le TAB fle 48 E file idval dx dy dz ds index valrd step dx dy dz 0 dD step ds
161. step cond endrd part m s xyzz N x y z x y z m s x 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 MC 2388751390 Pa 3583873590 Pa 59885444 Pa 3570441669 Pa step elem No Name Weight au 1 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 60 CC 6 871310355572089e 02 2 333598199034652e 09 1 28984832616168
162. nature 1 16 00 2 000 Busing 1 6 A 0 080 A Busing 1 a 2 b pm WA par 9 0 0 Busing nature Busing pair 1 1 Busing 3 344 A 0 160 A Busing 1 a 2 b pm
163. 5 RYUDO pair Angell 1 1 Angell 1 0 0 16 A 3 4 A 0 16 A 0 78 0 98 Angell Ai bibi gto oi Ci Di 28 pm pm pm pm kJ moll pm kJ moll Pauling 4 1 nN MN z n Cij Dijji E ff 2 E E C E w 2 4e A nature o E 1 N Angell RYUDO
164. Ver 1 17a 15 3 3 3 15 3 3 1 2 0 1 012 01 1 2 3 b 2 1 2 3 b 23 3 m 123 b In a
165. cutoff 3 4 cutoff 300 500 pm cutoff Zap 1 3 cutoff cutoff E cutoff 500 pm 32 2
166. text 2 for rd tps rd axis defird text 3 end N thc rd defrd cond Step Temp LoTemp HiTemp LowEnergy J HighEnergy J LowEnergyS J HighEnergyS J 100 370 9 278 4 524 4 6 0984449e 20 1 0929429e 19 0 0000000e 00 0 0000000e 00 200 431 4 334 0 455 1 1 5301740e 19 3 2068997e 19 0 0000000e 00 0 0000000e 00 300 439 8 274 2 492 1 6 5430227e 19 3 6493591e 20 0 0000000e 00 0 0000000e 00 3700 460 3 285 5 477 6 8 6984698e 20 1 4413814e 19 2 4134119e 18 1 8054827e 18 3800 319 2 297 9 481 6 6 1897632e 21 4 6184647e 20 3 0872629e 18 9 1692270e 19 3900 381 4 268 3 577 4 1 5795278
167. 1 0 1 0 0 LJ Busimg Angell FFF EL 15 nature 1 1 2 2 Busing Morse 2 800 A 12 0 kcal mol 0 160 A 1 980 1 A 2 880 A 1 2 Busing Morse
168. FF Types 64 define ELEMS MOLES ATOMS FF Types FFTTS MaterialsStudio car mdf F1 rdect Ver D RYUDO Ver 1 10a 1 12b end rd 3 RYUDO end rd 1 256 r
169. osr rd 0 0 1 0 RYUDO 50 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
170. pos rd pos2 rd 58 pos rd pos2 rd RYUDO mm s 1 2 5 2 x y z 3 5 3 Im s 16bit vel rd 32768 32767m s vel2 rd 10000 0 9999 16bit 4 16bit 8bit 8bit velrd vel2 rd 5 8bit 1 1 8bit vel2 rd 10000 2bit vel rd vel2 rd def rd step
171. 1 2 3 4 5 6 7 7 7 RYUDO set rd
172. 1 rdset rdset set rd set rd RYUDO cartesian Ver 1 08 Ver 1 19 detrd b RYUDO 2 2 RYUDO 4
173. 7 14 Ver 1 18 DD RYUDO RYUDO RYUDO defLrd atom hybrid
174. E defLrd set rd CPU 1CPU 2 1 2 RYUDO bat rd 1 1 end
175. H single i me 3 3 E 2 E cutof E NO E single
176. rdmov Ver RYUDO end rd X Y Z m gcc rdmov c o rdmov endrd rdmov rdmsp Ver 1 03a TRIBOSIM MSPORT RYUDO file05 dat def rd bondon dat bnd rd setrd
177. RYUDO 7 11 RYUDO defrd files text fles text 100 100 100 tps rd tvl rd rd
178. StatusElement 1 8 FF Type 2 0 car 5 rst h FF Type 7 SubFFType rst 6 car BIOSYM NameMolecule car EndMolecule 0 3 MoleculeFrom1 rst elem 67 E 1 end 1
179. 1 2 i 1 2 RYUDO 1 1 255 1 2 _ 3 E 2 2 A
180. 3 K C K F step E Ver 0 86 10 Ver 0 85 def rd 1 step 9 press F 10 RYUDO
181. Inature trio nature pair 3 j 3 3 set rd 2 Ve
182. set rd part 2 1 MSD mc msd mm msd 2 pos rd pos rd 1 2 9 7 8 7 9 2 Ver 1 10 id temp id msd el te id 3 Ver 1 10 id temp val rd 3 Ver 1 11
183. 3 E E 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
184. B Angell Angell Busing Busing Busing c d d c d c 14 2 2 table pair parr Busing Busing Bwald
185. 2 90 3 90 RYUDO 90 Ver 1 03 gcc rdrho c o rdrho Im math rdrho rst P1 car rst 1 100 100 w 90 2 car
186. 3 4 RYUDO 4 Coulomb L RYUDO CVFF 6 5 2 SW SW 2 3 lt RYUDO
187. appear appear MA 2 set rd 4 end rd ad appear option appear3 appear4 7 8 RYUDO 1
188. def rd rd82t87 rd82t87 gt def new OA ON DE TO OO NRN DO NRG ON Ver 0 50 def rd 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 def rd
189. g kJ moll al c pm 6 2 3 33 HzO 3 2 cos 2 9 9 11Y 6 ki kz jj 17texplg 7og 07 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
190. 19 19 14 14 15 5 16 16 17 A t 1 step si mx step end rd val rd pos rd vel rd for rd tmp rd cutoff 2 cutoff 3 cutoff Ewald 3
191. HH 3 4 8 cutoff CVFF 1 8 E RYUDO 253 3 4 3 0
192. 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
193. 3 off 0 Ewald 3 Ewald 3 RYUDO 3 pair Coulomb 11 atom 2 RYUDO 12 E
194. J m defLrd atom atom 1 1 1 0 0 50 0 6 m 1 50 0 m2 0 1 m 0 1 m 0
195. 2 n x yw cos c n c 100 x y 90 n Qr NT rdext Ver 1 03 64 RYUDO rst x y z Ver 1 02 rdext rst x AN
196. file05 dat defrd rdcar Accelrys car mdf Ver 1 14a Cerius2 MaterialsStudio rst gcc rdcar c o rdcar Im math H 3 RYUDO car mdf rdcar abc car abc mdf rdcar rst abc mdf rst
197. 1 val rd more Excel m E B xtr rd Ver 1 13 61 E bondon dat bnd rd E step 2 00
198. 1 m fkx fy fs index valrd step 9 fx fy 0 fs val rd lid fz index 1 N ftx fty ftz fs index val rd step step ftx fty ftz fts
199. 1 y 1 0pm 1 move 1 move 1 0 pm 0 0 1 pm 0 nmove x y z x y z pm 1 x 1 0pm 2 1 1pm 1 0 1pm ie
200. def rd set rd F Rl o mc msd mm msd 3 MSD mz 0 1 2 MSD set rd 0 1 4 3 0 1 4 defi h define MOLESD 3 mc msd mm msd mc msd 1 mm msd 2 pos rd
201. 10000 2bit for rd for2 rd def rd step tmp rd defrd iles 5 pos rd 1 K 2 16biD 3 16bit 8bit 8bit 4 8bit 1 1 8bit 5 1 4 tmp rd defrd
202. CVFF y z 3 0 gt J rduni Ver rst RYUDO H
203. HH MS Windows MS DOS ky set rd step x y z x a h p S date defLrd files 1 0
204. atom atom 1 1 1 0 0 0 2 2 2 0 0 0 X 1 2 0 0 K 0 RYUDO 0 K 1 rr r U H r ro H
205. eV erg e A A 6 lu m c k M G m 3 18 RYUDO kcal mol disp 2 Out of Plane 4
206. step step x y z step x y 2 fix on 3 off 1 2 3 1 2 3 set rd atom atom 1 2 parr
207. 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
208. 2 NI i 7 Ewald ewald NS 2 cutoff j 2 Coulomb RYUDO Ewald 3 off 1 2 Ewald H 10
209. f NBW RYUD O CO E NEW E 2 RYUDO Linux RYUDO make
210. rdtxt RYUGA rdsum Ver 1 01 RYUDO gcc rdsum c o rdsum Im math H
211. Torsion 4 ut of Plane ke 17 1 2 1 3 3 2 4 4 2 Torsion
212. 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
213. move single 2 move 1 0 pm single move single move atom set rd move x y z pm 10 m Ver 1 05 pm 41 2
214. 0 4 mi 4 disp 1 1 Gndexy MSD atom nature index x y z
215. 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
216. 4 6 3 4 5 6 3 4 4 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 1 0 GPa RYUDO
217. 0 050e 20 274 0 1 ce 2 0 pair nature pm 26 Kong RYUDO Ljk 12 Ei yy 13 2 12 1 13 LO 1 2 ll Me EO OE nature J m nature pair nature LJ AB g o LJ
218. 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 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
219. 56 162731 38 0 000 26 200 23 560 70 000 7 13 52 44 49 791 0 0 788 162651 69 0 000 26 200 23 560 70 000 7 13 52 44 50 818 6 1 311 162437 28 0 26 200 23 560 70 000 7 13 52 44 000 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 13 52 45 y 7 52 817 2 1 912 162810 00 0 000 26 200 23 560 70 000 7 13 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 55 823 7 0 109 162543 39 0 000 26 200 23 560 70 000 7 56 793 7 0 182 162767 59 0 000 26 200 23 560 70 000 7 1 aa defrd disp 1 2 3 1
220. 712974 0 624992622099729 0 420209015130551 0 079637341568431 0 580156552893353 0 311948823415684 0 496064029308648 0 050091092422330 0 948095661608534 0 549524764418257 0 056679868129164 0 942979639945443 0 556768906929942 0 326293497674753 0 496622787387862 0 758921370698567 0 258614294663550 0 238933083162002 0 665440308805454 0 165512978234313 0 333552217372585 0 180830886822238 0 002929194691235 akis m 1 No x y z def rd text 1 tps rd axis end tvl rd vel rd E vel rd
221. 9e 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 defi h define EXTPVFOUT 0 pos2 rd pos2 rd pos rd Ver 1 19 3 0 2 0 3 0 2 0 62 10 RYUDO
222. BOSIM MSPORT 2 Cerius2 rdset au 3 Sm car 9 Car car 2 E E set rd rd set rd step data cond 80 80 part 80 set rd
223. H 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
224. J moll 35 6 4 Out of Plane 4 3 2 x RYUDO Out of Plane 1 j k 1 i j k 1 ik il x Out of Plane G k 1 6 4 1 Out of Plane MD
225. Out of P quad ane 4 3 defrd RYUDO Out of Plane F tetra tetra 1 4 Torsion 4 tetra table
226. YUDO RYUDO NEW RYUDO NEW RYUDO NEW RYUDO NEW RYUDO RYUDO RYUDO 70
227. d 10000 0 9999 4 pos rd 3 2 10000 30000 29999 3 2 6 10000 pos2 rd dl IGT l 5 8bit 8bit pos rd pos2 rd 6 8bit 1 1 8bit 0 0 1 0 0 10000 pos rd pos2 rd MSD 1 16bit 3 2
228. dect end rd end1 rd 256 gcc rdect c o rdect rdect end rd end1 rd end1 rd o lt rd82t87 Ver 1 01 defrd Ver 0 82 Ver 0 87
229. e 1 0e 9 N 0 0 N 0 0 N 1 0e 10 N 0 0 0 0 force x y z x y z N 1 x 1 1 0x10 N 2 1 1x10 N 1 1 0x10 N 7 5 RYUDO def rd single
230. e 19 2 5398951e 19 2 8283404e 18 1 1536329e 18 4000 325 6 303 9 451 5 8 3655205e 21 1 4247757e 19 3 5672638e 18 1 0859657e 18 60 SS co log rd RYUDO scr rd RYUDO 1 7
231. r 1 11c atom atom 0 atom 3 E Ver 1 11d E RYUDO DW 54
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