Index
A
B
C
D
E
F
G
H
I
J
L
M
P
R
S
T
U
W
Y
Z
- 2D-periodic structures 27
- 3D-periodic structures 5, 79
A
- Add Atom control panel 12, 15, 33, 34
- amides 83
- AMORPHOUS BUILDER card 74
- Amorphous Builder Clone control panel 82
- Amorphous Builder control panel 77, 78, 88
- Amorphous Builder module 73
- Amorphous Builder Output control panel 78
- Amorphous Builder Preferences control panel 78, 88
- Amorphous Builder State Table control panel 85, 88
- Amorphous Builder Torsions control panel 83, 84
- amorphous structures 73
- 3D-periodic 75, 79
- aborting a build 80
- anomalous behavior during builds 84
- building 74
- building in general 78
- building with default settings 77
- bump checking 75, 78, 79
- bump checking, hydrogens 79
- cloning starting structures 82
- display 81
- finding unique rotatable torsions 84, 85
- minimization conditions 81
- minimizing 80
- Monte Carlo method 75
- nonperiodic 79
- periodic density 78
- relaxing 76, 80
- repeated building attempts 76, 79
- RIS methods 75
- rotatable torsions 83
- rotation methods 86
- saving 81
- simple build 77
- starting a build 81
- stopping a build 80
- torsions 78, 83
- torsions used during building 87
- troubleshooting 80
- unique torsions table 85
- van der Waals scale 75
- Amorphous Torsion Rules control panel 83
- asymmetric unit 7
- constructing 8
- atoms
- adding 14, 34
- backbone 52, 68
- converting symmetry copies into real 16
- coordinates 42
- deleting symmetry copies 19, 36
- display 70
- exact symmetry positions 24
- groupings in polymers 69
- names 83, 84
- options 15, 34
- removing 15, 18, 34
- selecting in crystals 22, 23
- superimposed 44
B
- biphenyl 83
- Block Copolymer Builder control panel 66
- Block Copolymer control panel 59
- Block Copolymer Preferences control panel 66
- block copolymers 47, 66, 69
- building 66, 68
- composition 66
- number of superunit blocks 67
- preferences 67
- superunit groupings 69
- superunit size 67
- bold type, meaning 3
- bond arrays, sorting 84
- bonds
- automatic calculation 9, 31
- crystals 9
- dangling 43
- interfaces 43
- multiple 83
- surfaces 30, 31
- Bravais lattices 10
- BUILDERS 1 card deck 7, 29, 38, 48, 74
- Building From Atoms control panel 31, 33, 35, 36, 45
C
- Cell Contents control panel 23
- Cell Parameters control panel 9, 12
- Cleave Crystal Surface control panel 29, 35
- Convert Formats control panel 54
- coordinate system 14
- fixing 34
- coordinates
- Cartesian 14, 33
- crsytal interfaces 39
- fractional 14
- orientation to computer screen 20
- surface fractional 33
- copolymers 47, 60, 66
- Crystal Build Preferences control panel 8, 11, 12
- CRYSTAL BUILDER card 7
- Crystal Builder module 5
- Crystal Building control panel 8, 11, 12, 17, 18, 19, 45
- Crystal Facetting control panel 18, 22
- Crystal Visualization control panel 17, 20, 21
- crystals
- accuracy of model 23
- asymmetric unit 8
- bonds 9
- building 7
- cell size and shape 9
- cell volume 23
- connectivity 10
- constructing from atoms 12
- creating from interfaces 38, 45
- default orientation 20
- defects 37
- density 23
- disorder 17
- display 19
- display range 19
- display style 9, 11, 13
- facetting 18, 22
- faults 39
- from surface 11
- generating nonperiodic superstructures 16
- generating superlattices 16, 17
- habit planes 20
- initial orientation 19
- interfaces 37
- lattice 10
- Miller planes 20
- nonperiodic model 17
- number of displayed cells 20
- polymer 6
- polymers 56
- redisplaying 12
- reverting to nonperiodic asymmetric unit 19
- sectioning 22
- selecting atoms 22
- simulations 5
- structural relationships between particles 37
- symmetry 9, 10, 12, 13
- twinning 37, 39
- unbuilding 19
- unit cell, constructing 13
- updating 12, 24
- vacuum slab 11
- vacuum thickness 11
D
- Display Editor control panel 70
- Display Preferences control panel 70
E
- Edit Facet Options control panel 22
- Edit Interface control panel 44
- epitaxy 37
F
- facets
- adding 22
- color and transparency 22
- creating 22
- crystal 22
- displaying 22
- editing 22
- positioning 22
- removing 23
- files
- 2D unit cell information 28
- Biograf 54
- conversion 53
- CSSR 28
- example .ris 97
- formats 95
- Insight II 54
- monomers 53, 54
- MSI 28
- old Cerius2 54
- Polygraf 54
- .ris 87, 91, 95
- rotatable torsions 95
- state table 95
- surface information 28
- trajectory 79, 81
- Find Space Group control panel 11, 24
- Flory, P. J. 86, 93
G
- General Positions control panel 9
H
- help, on-screen 3
- high-resolution transmission electron microscopy 37
- Homopolymer Builder control panel 55, 58, 59
- Homopolymer Preferences control panel 55
- homopolymers 47
- atomic groupings 69
- building 55, 56
- composition 55
- preferences 56
I
- INTERFACE BUILDER card 38
- Interface Builder module 37, 38
- Interface Building control panel 43
- Interface Left Side control panel 41
- Interface Right Side control panel 41
- interfaces
- alignment of sides 40
- building 44
- creating crystals from 45
- creating surfaces from 45
- crystal 37
- duplicated atoms 44
- editing 44
- gap 43
- match point 40, 42
- match vector 40, 42
- Miller indices 42
- Miller planes 41
- orientation of sides 40
- periodicity 40
- setting up 41
- shape 40, 42
- slab thickness 42
- superimposed atoms 44
- vector conventions 39
- italic type, meaning 3, 4
J
- Jackson, C. J. 93
L
- lattice
- Bravais 10
- infinite assumed 20
- primitive 16
- reorienting 15
- specifying 9
- symmetry 10
- type 10
- Lattice Redefinition control panel 15
- lattice vectors
- changing 15
- display 16
- new 15
- previewing changes 15
- redefining 15
- user-specified 15
- Load State Table control panel 87
M
- methyl rotors 83
- Miller indices 21
- Miller Plane Options control panel 21
- Miller planes 20
- color 21
- display 21
- facetting along 22
- opacity 21
- positioning 21
- reorienting 21
- transparency 21
- models
- 2D periodic 11, 27
- amorphous 73
- copying 82
- crystal 5
- crystal interfaces 37
- ionic 6
- monomers 52
- multiple-chain 82
- polymers 6, 47
- surface 11, 27
- Molecular Simulations, Inc.
- customer support 3
- website 3
- molten state 73
- monomer choosers 50
- Monomer Editor control panel 51, 52, 54
- Monomer Orientation control panel 59
- Monomer Preferences control panel 51, 52
- Monomer Reactivities control panel 65
- monomers 49
- available to polymer builder 50
- backbone atoms 52
- chiral centers 49, 52, 53, 57
- chirality 49
- choosing types 55, 61, 66
- color use 70
- concentrations 62
- concentrations, exact 63
- creating 50
- definition 49
- display 70
- editing 52
- files 49, 50
- head group 49, 51, 70
- head/tail orientation 56, 58, 62, 67
- inversion at chiral center 49, 53, 62
- labelling 70
- loading 51, 52, 53
- number of units 55, 61
- reactivities 62, 63
- reactivity ratios 64, 65
- relative concentrations 60, 62
- relative reactivities 60, 62, 65
- saving 53
- tail group 49, 51, 70
- torsions between 51, 56, 59, 62, 67
- torsions within 59
P
- POLYMER BUILDER card 48
- Polymer Builder module 47, 48
- Polymer Editor control panel 68
- Polymer Tacticity control panel 58
- Polymer Torsions control panel 60, 66
- polymers
- atactic 58
- atomic groupings 69, 71
- backbone atoms 68
- backbone display 70, 71
- building 47, 61, 66
- chemical nature 69
- chiral centers 68, 71
- color use 70, 71
- configuration 49, 57
- copolymers 60, 66
- crystals 56
- display 70
- editing 68
- filenames 64, 67
- grouping classes 69
- grouping types 69
- head group 70
- initiator 55, 61, 67
- inversion at chiral center 68
- isotactic 58
- labelling 70, 71
- levels of atomic groupings 69
- meso-diad ratio 58
- monomer units 49, 61
- names 64, 67
- of polymers 63
- random-number generator 56, 63, 67
- stereoconfigurations 57
- structure 69
- superunit blocks 67
- syndiotactic 58
- tacticity 56, 57, 62, 67
- tacticity, illustration 57
- tail group 70
- terminator 55, 61, 67
- torsion between monomer units 49, 56, 59, 62, 67
- visualization 70
R
- Random Copolymer Builder control panel 59, 61, 63, 65
- Random Copolymer Preferences control panel 63, 65
- random copolymers 47, 60
- building 61, 62
- composition 61, 64
- preferences 62
- rate constants 64
- RIS energy method 75, 89, 90
- temperature 89
- RIS methods 73, 78
- number of states 89
- specifying 87, 89
- tolerance 86, 89
- tolerance scale factor 86, 89
- RIS ratio method 75, 89, 90
- RIS variables 85
- rotational isomeric state methods 73
S
- Save State Table control panel 91
- semicrystalline state 73
- single-bond sp2-sp2 interactions 83
- solution 73
- solvent 6
- space group
- cell origin 14
- class 13
- example specifications 14
- hexagonal axes 14
- information 13
- monoclinic 14
- name 13
- nonstandard 13
- number 13
- options 13, 14, 24
- reference 13
- rhombohedral axes 14
- specifying 13
- standard 24
- symbol 13
- Space Groups control panel 12
- superlattices
- generating from crystals 16, 17
- generating from surfaces 35
- primitive 17
- size 17, 35
- unit cell 18
- superstructures
- generating from crystals 16
- generating from facetted crystals 18
- generating from surfaces 35
- noncrystalline 18
- nonperiodic 17, 18, 19, 35
- previewing 23
- size 18, 35
- Surface Box control panel 29
- Surface Build Preferences control panel 31
- SURFACE BUILDER card 29
- Surface Builder module 27
- surface cell
- deleting 36
- dimensions and angles 32, 33
- Surface Cell Parameters control panel 31, 33, 34, 45
- surface cell vectors
- changing 34
- new 35
- redefining 34
- Surface Visualization control panel 35, 36
- surfaces
- basis vectors 30
- bonds 30, 31
- cell, constructing 32
- cleaving slab 29
- constructing from atoms 33
- creating from crystals 29, 31
- creating from interfaces 38, 45
- creating from nonperiodic models 31
- disorder 35
- display 30, 36
- display range 36
- display style 32
- generating nonperiodic superstructures 35
- generating superlattices 35
- Miller indices 30
- number of displayed surface cells 36
- positioning slab 30
- redisplaying 32, 33
- reverting to nonperiodic asymmetric unit 36
- slab shape and position 30
- surface cell, constructing 33
- thickness 30
- unbuilding 36
- updating 30
- symmetry
- cell parameters 10
- constraints 9, 14
- constraints, removing 17
- crystal 9, 12, 13
- editing 10
- exact match of atom positions 24
- finding 12, 24
- positions 10
- primitive 17
- reducing 15, 16
- reimposing 24
- tolerance 24
T
- torsions
- acceptable 79
- build methods 78
- chirality 83
- coupling 85, 86, 90
- display 70, 85
- excluded 83
- file 95
- fixed 86, 89
- information 88
- labelling 70
- range of angles 89
- renaming 85, 88
- rigid 86
- rotatable 83
- rotation methods 78, 85, 87, 88, 89
- rules 83, 85
- searches 84
- sorting 84
- state table 87
- states 89
- types 85
- unique rotatable 78, 83
- unique torsions table 87
- typewriter font, meaning 3
- typographical conventions 3
U
- unit cell 6
- changing to primitive 15
- constructing 13
- deleting 19
- density 23, 79
- dimensions and angles 9, 14
- formula 23
- information 23
- number displayed 19
- number of atoms 23
- volume 23
W
- Wood, J. 93
Y
- Young, L. 64, 93
Z
- zeolite structures 6
Last updated April 06, 1999 at 04:19PM Pacific Daylight Time.
Copyright © 1999, Molecular Simulations Inc. All rights
reserved.