TOMBO Ver.2 Manual

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5.2 Molecular Dynamics 53 Table 5.2 INPUT.inp of Fe 2 line 1 SYSTEM=Fe2 line 2 iApp =LMNN line 3 iAlg =D line 4 nod =14 line 5 ncs =0 line 6 noz =64 line 15 icontinue =0 line 16 isphcut =-1 line 17 iTotalE =1 line 18 lpri =1 line 19 nspin =6 line 20 iMIX =0 line 21 smixSCF =0.90 line 23 iSblp =300 line 26 iasym =0 line 27 icalAO =0 line 28 iCry =0 line 29 iExcite =0 line 30 precLDA =0.000001d0 line 31 iFTapp =0 line 32 iCheb =0 line 33 nstep =1 line 34 END_PARA 5.2 Molecular Dynamics As an example of a first-principles molecular dynamics simulation, Fig. 5.4 shows several snapshots of a chemical reaction producing a formic acid (HCOOH) molecule from a carbon dioxide (CO 2 ) molecule and two hydrogen atoms (2H) [2]. In this MD simulation, COORDINATES.inp file given in Table 5.3 and INPUT.inp files given in Table 5.4 are used.
5.2 Molecular Dynamics 54 Fig. 5.4 Snap shots of a molecular dynamics (MD) simulation producing HCOOH from CO 2 + 2H. Table 5.3 COORDINATES.inp of 2H + CO 2 line 1 CO2+H2=>HCOOH line 2 8.000000000000 line 3 1.000000000 0.000000000 0.000000000 line 4 0.000000000 1.000000000 0.000000000 line 5 0.000000000 0.000000000 1.000000000 line 6 2 line 7 Cartesian line 8 C 1.2000000000 0.0000000000 0.0000000000 line 9 O 0.0000000000 0.0000000000 0.0000000000 line 10 O 2.4000000000 0.0000000000 0.0000000000 line 11 H 1.2000000000 1.7000000000 0.0000000000 line 12 H 2.4000000000 -1.7000000000 0.0000000000 line 13 C _rct=0.60 line 14 C _ns=2 line 15 C _np=1 line 16 O _rct=0.50 line 17 O _ns=2 line 18 O _np=1 line 19 mesh=48 line 20 dTime=0.1d0 line 21 END_PARA
Page 1 and 2:
TOMBO Ver.2 Manual for LDA and GW C
Page 3 and 4:
Table of contents 1 Introduction 1
Page 5 and 6:
Table of contents v 3.2.42 Mcheb .
Page 7 and 8: 1.2 Mixed basis formulation 2 to th
Page 9 and 10: 1.2 Mixed basis formulation 4 Many-
Page 11 and 12: 1.3 All-electron charge density and
Page 13 and 14: 1.3 All-electron charge density and
Page 15 and 16: 1.4 Calculation flow 10 1.4 Calcula
Page 17 and 18: 1.5 TDDFT dynamics simulation 12 of
Page 19 and 20: 2.2 The Green function 14 2.2 The G
Page 21 and 22: 2.4 Hedin’s equations (GWΓ metho
Page 23 and 24: 2.5 The GW approximation 18 The GW
Page 25 and 26: 2.6 One-shot GW approximation 20 or
Page 27 and 28: 3.1 COORDINATES.inp 22 3.1 COORDINA
Page 29 and 30: 3.1 COORDINATES.inp 24 10. The Atom
Page 31 and 32: 3.2 INPUT.inp 26 3.1.1 rct "XX_rct"
Page 33 and 34: 3.2 INPUT.inp 28 An example of INPU
Page 35 and 36: 3.2 INPUT.inp 30 3.2.5 Ulevel, Llev
Page 37 and 38: 3.2 INPUT.inp 32 calculation of the
Page 39 and 40: 3.2 INPUT.inp 34 Whether the subtra
Page 41 and 42: 3.2 INPUT.inp 36 3.2.30 smixSCF Cha
Page 43 and 44: 3.3 KPOINT.inp 38 3.2.42 Mcheb Numb
Page 45 and 46: 3.4 QPOINT.inp 40 10, line 15, and
Page 47 and 48: 3.5 SPOINT.inp 42 Table 3.9 QPOINT.
Page 49 and 50: Chapter 4 Output Files Note: 1. In
Page 51 and 52: 4.8 WaveF_HOMO-1.cube, WaveF_HOMO-1
Page 53 and 54: 4.9 GWA.out 48 Table 4.2 GWA.out of
Page 55 and 56: Chapter 5 Examples 5.1 LDA calculat
Page 57: 5.1 LDA calculation of isolated dim
Page 61 and 62: 5.4 LDA calculation of rutile TiO 2
Page 63 and 64: 5.4 LDA calculation of rutile TiO 2
Page 65 and 66: 5.5 Wave function calculation of ru
Page 67 and 68: References 62 [12] M. S. Bahrany, M
Page 69 and 70: A.1 Build crystal model 64 A.1 Buil
Page 71 and 72: A.3 *.cell file 66 Fig. A.4 1 st Br
Page 73 and 74: A.3 *.cell file 68 Step 4 In "CASTE
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