Index
A
B
C
D
E
F
G
H
I
L
M
N
O
P
Q
R
S
T
U
V
Y
Z
A
- accumulate averages of mechanical properties 6
- alignment of polymers
- measuring 39
- alloys, polymer, see Blends
- all-trans conformation 79
- analysing trajectory files 149
- analyzing
- stress/strain data in Mechanical Properties 14
- applied strain table 10, 12
- applied stress table 10, 11
- asymmetric unit 128, 130
- defining molecules in the 134
- atomic correction terms 89
- atomic indices 86
- atomistic interactions 85
- averaging
- of mechanical properties 6
- axial packing for Blends 63
B
- backbone
- flags 94, 96
- torsion 101
- bad contacts check in Crystal Packer, see close contacts
- bad contacts check in Sorption 232, 235
- Biased Metropolis averaging in Pairs Method for Blends 60
- Bicerano, Dr. Jozef 69
- binodal curve, see phase diagrams
- Blends interaction energy (.enr) files 44
- analysis of 49, 53
- extracting molecular pairs from 53
- loading 48, 54
- saving 45
- Blends module 41-67
- analysis functions 43, 65
- applications for 42-43
- calculation functions 43, 58
- interaction parameter 55, 63, 64
- phase diagrams 57, 65
- theory 56-57
- Boltzmann averaging in Pairs Method for Blends 59
- bond indices 87
- bond selection rules for polymer orientation function 32
- branched polymer chain 98
- bulk modulus
- definition 17
- to calculate, see mechanical properties
- bump check, see bad contacts check
C
- calculating
- chain properties of polymers 23
- coordination numbers 45
- crystal energy 116
- dihedral angle distributions in polymers 26
- enthalpy of mixing 51
- entropy of mixing 51
- free energy of mixing 51, 66
- interaction parameter 65
- mechanical properties 5
- phase diagrams, two component 65
- physical properties of polymers 23
- polymer orientation functions 38
- Voronoi volume of polymers 25
- canonical ensemble sorption simulation, see fixed loading
- catalysts database 231
- cell parameters
- constraining during Crystal Packer minimization 112
- chain connectivity 88
- chain continuation 86
- charges, ESP 130
- Chi, see interaction parameter
- CIF file format 322
- cluster analysis 128, 144
- procedure 144
- cluster analysis preferences
- clustering parameters 146
- input file 145
- output options 147
- cluster, lowest energy representative 128
- clustering energy minimization output 144
- clustering Monte Carlo output 144
- cohesive energy 80, 89
- combination rules, see VDW energy term
- comparing powder spectra 151
- compliance matrix 2
- definition 17
- to calculate, see mechanical properties
- compressibility, see volume compressibility
- connectivity indices 69, 86, 87
- backbone 89
- first-order (bond) 88
- side group 89
- zeroth-order (atomic) 87
- constant strain minimization (for property prediction) 4
- setting up 9-12
- constant stress minimization (for property prediction) 3
- setting up 9-11
- constraints for Crystal Packer minimization 112
- contact table, see nonbond list
- contributions 80
- convergence accelerating smearing 119
- coordination numbers in blends 55, 61
- procedure for calculating 45
- copolymer, statistical 69
- correlations, general forms of 89
- Coulomb energy calculation in sorption 234, 236
- Coulomb energy term, Crystal Packer 120
- crystal constraints, effect on mechanical properties 7
- determining 9
- crystal modifications 157
- Crystal Packer module 105-126
- curve fitting, see data fitting
D
- dat files
- output from Mechanical Properties 13
- data fitting (Mechanical Properties) 15
- defining space groups 143
- degree of polymerization 55
- density of polymers 34
- deriving mechanical properties 17
- Designer Correlations 81
- dihedral angle distributions in polymers 26
- selecting torsions 26
- torsion selection rules 28
- dihedrals, see also torsions
- dipole moment 100
- dipole moment in polymers 33
- displaying
- mechanical properties 12
- Dow Units 81
- Dreiding force field 130
E
- electronic environment 86
- electrostatic interactions 130
- electrostatic, see Coulomb
- empirical and semi-empirical methods 69
- end-to-end distance
- probability distribution 99
- end-to-end distance of polymers 36
- energy
- minimization, see minimizing
- procedure for setting up Crystal Packer calculation 108
- setting calculation for Crystal Packer 117
- setting calculation for Mechanical Properties 19
- setting calculation for Sorption 232
- energy distribution histogram, sorption 247, 250
- energy expression in Crystal Packer, setting up 117
- energy minimization 129, 147
- optimizing the current model 147
- energy of mixing
- fitting 64
- enthalpy of mixing
- calculating and plotting 51
- entropy of mixing
- calculating and plotting 51
- ESP charges 130
- Ewald long-range summation method 130
- Ewald summation method
- in Crystal Packer 109, 121
- in Sorption 234, 236
- excluded atom constraints in Blends packing 64
- excluded volume constraint, Blends 59
- extensive property 89
- additive constant term 89
- extracting models from trajectory files 149
F
- Fedors-like, cohesive energy 80
- file formats
- crystal morphology 322
- interactions.dat 324
- files
- .arc 99
- .rislog 99
- .rismnt 99
- .tab 99
- _dih.tbl 99
- _pr.tbl 99
- _rsq.tbl 99
- finding probable crystal structures 159
- fixed loading sorption simulation 230, 253-254
- fixed pressure sorption simulation 230, 254-256
- flexible molecules 132
- flexible molecules, handling 131
- Flory-Huggins model for polymer blends 54-55
- force field
- Crystal Packer's own 105, 117
- for Blends calculation 57
- for mechanical properties 19
- for sorption simulation 231, 235
- force fields 132
- free energy of mixing 55
- calculating 51, 66
- plotting 51
- fugacity in fixed pressure sorption simulations 254
G
- Gaussian ab initio quantum mechanics package 130
- geometrical parameters 89
- grand canonical ensemble sorption simulation, see fixed pressure
- graph
- hydrogen-suppressed 86
- graphs
- applied strain profile (Mechanical Properties) 12
- applied stress profile (Mechanical Properties) 11
- Blends pair energy analysis 49
- Crystal Packer energy 116
- energy of mixing 65
- interaction parameter
(T) 65 - phase diagrams, two component 65
- polymer dihedral angle plots 26
- polymer orientation angle histogram 30
- polymer orientation vector vs. time 30, 32
- polymer properties vs. time 24
- sorption analysis 245
- sorption output 237, 239
- thermodynamics of mixing 51
- Voronoi volume vs. time 37
- group additive methods 75, 85
- group contributions 69
- group correction terms 89
H
- H-bond energy term, Crystal Packer 121-123
- Henry constant sorption calculation 230, 256-258
- Hermans orientation function, see orientation function
- homopolymer, bulk amorphous 69
- hydrogen-suppressed graph 86
- hydrostatic energy term, see pressure term
I
- indices
- atomic 86
- bond 87
- connectivity 86
- valence 87
- initialization of model in Crystal Packer 107
- intensive properties 89
- interaction energies
- file format 324
- interaction energies, see pair interaction energies
- interaction parameter
- calculating and plotting 64
- definition of 55
- expression for 63
- interactions.dat file format 324
- interrupting
- a sorption simulation 244
- intramolecular symmetry 133
- isotherms, sorption see loading curve 247
- isotherms, thermodynamic for Blends 52
- to plot 53
- isotropic packing for Blends 63
L
- Lamé constants
- equation for 18
- to calculate, see mechanical properties
- lattice cluster theory for polymer blends 55
- Lennard-Jones functional form 119
- liquid crystal polymers
- orientation function of 38
- packing variables for Blends 60, 64
- loading
- Blends interaction energy (.enr) files 48, 54
- Mechanical Properties .mp files 16
- off-diagonal VDW pair potentials file 120
- on-diagonal VDW pair potentials file 120
- trajectory file for Polymer Properties analysis 22
- loading curve, sorption 247, 251
- lowest energy cluster representative 128
M
- macromolecules, see polymers
- mass clouds, sorption 248, 252
- mass distribution plot, sorption 246, 250
- Max Bonds 95
- mechanical properties 1, 69, 79
- analyzing stress/strain data 14
- calculating 5
- deriving from stiffness matrix 17
- models for calculating 19
- output 6, 12
- prediction methods described 2-18
- saving data to file 12
- Mechanical Properties module 1
- merging trajectory files 155
- Metropolis algorithm 138
- Metropolis averaging in Pairs Method for Blends 60
- Metropolis selection in sorption simulation 253
- Min Bonds 95
- minimization algorithms 113
- Modified Newton 113
- Steepest Descent 113
- minimization preferences
- input file 147
- output options 148
- termination criteria 147
- minimizing, crystal energy 106, 112
- constraints setup 112
- setup for 113
- minimizing, in Mechanical Properties
- model first 6
- under constant strain, see constant strain minimization
- under constant stress, see constant stress minimization
- minimum image convention 233
- mixing energy, see energy of mixing
- mixtures
- polymer-polymer, see Blends
- polymer-solvent, see Blends
- solvent-solvent, see Blends
- model initialization, Crystal Packer 107
- model window
- sorption updates 237, 238
- modifications, crystal 157
- Modified Newton, minimization algorithm 113
- modulus
- see bulk modulus
- see shear modulus
- see Young's modulus
- molar
- heat capacity 89
- volume 89
- molecular pair configurations 44
- energy distribution 49
- selection by energy 53
- molecular properties 86
- molecular silverware algorithm 59
- molecular weight of polymers 34
- Monte Carlo packing simulation 128, 138
- trial steps 139
- Monte Carlo preferences
- output options 144
- search parameters 141
- space groups to searcb 142
- morphology of crystals
- file format 322
- move probabilities, sorption 240
- mp files for Mechanical Properties 321
- msi model files output by Mechanical Properties 321
N
- nearest neighbors packing in Blends 62
- nonbond list
- updating during minimization
O
- off-diagonal VDW parameters 120
- on-diagonal VDW parameters 119
- order parameter of polymers, see orientation function
- orientation angle, polymer 40
- orientation function, polymer 38
- bond selection rules 32
- calculating and plotting 29
- definition 39-40
- oriented polymers
- packing variables for Blends 60, 64
- output for sorption simulation 237
- output from Mechanical Properties module 6, 12
- analyzing 14
- msi model files 321
- reloading for analysis 16
- run parameter (.mp) files 321
- specifying 13
- table (.dat) files 321
- text (.txt) files 321
- trajectory (.trj) files 321
P
- packing calculations for Blends
- axial packing 63
- excluded atom constraints 64
- isotropic packing 63
- procedure to specify variables 46
- specifying variables 63
- packing calculations for crystals, see Crystal Packer module
- pair interaction energies 55
- calculating 58
- calculation output 60
- plotting distribution of 49
- procedure to calculate 44-45
- procedure to plot 51
- Pairs Method, Monte Carlo sampling for Blends 58-61
- Biased Metropolis averaging 60
- Boltzmann averaging 59
- Metropolis averaging 60
- permeability units 81
- persistence length 100
- phase diagrams, two component 57, 65
- .pmp files, see Polymorph Predictor trajectory files
- Poisson's ratio
- equation for 18
- to calculate, see mechanical properties
- polymer blends 41-67
- polymer properties
- density 34
- dihedral angle distributions 26
- dipole moment 33
- end-to-end distance 36
- estimation 69
- molecular weight 34
- quadrupole tensor 34
- radius of gyration 35
- Polymer Properties module 21
- polymer solutions, see Blends
- polymers, crystalline
- dimensionality in Crystal Packer 118
- polymers, liquid crystal
- Blends packing variables 60, 64
- polymers, oriented
- Blends packing variables 60, 64
- polymorph prediction 127-163
- polymorph prediction steps
- cluster analysis 144
- cluster minimized structures 129, 144
- energy minimization 128, 147
- Monte Carlo packing simulation 128, 138
- setup 128, 129
- polymorph prediction theory 158
- Polymorph Predictor limitations
- force fields 132
- intramolecular symmetry 133
- molecule flexibility 132
- processing speed 133
- Polymorph Predictor module 127-163
- Polymorph Predictor trajectory files 128
- analysis 149
- extracting models from 149
- merging 129, 155
- properties of structures in 149
- polymorphism 157
- potential of mean force 97
- powder spectra 151
- predicting polymorphs manually 136
- predictive correlations 85
- preparing models for polymorph prediction 130
- pressure term, Crystal Packer 125
- properties of polymers, see polymer properties
- property prediction, see mechanical properties
Q
- quadrupole tensor in polymers 34
R
- radius of gyration of polymers 35
- reliability checks 129, 156, 159
- repeat unit
- length computation 79
- rescaling step sizes, sorption 241
- restart files 133
- restarting interrupted polymorph prediction procedures 133
- rigid body minimization 148
- rigid units, Crystal Packer 106
- RIS Metropolis Monte Carlo
- computing dihedral distribution functions 98
- energy calculation 95
- output files 99
- parameters 96
- rotatable bonds 94
- RIS Metropolis Monte Carlo (RMMC) simulation 99
- RIS Monte Carlo
- properties calculated from 100
- RIS_Metrop_MC_Run command, RIS_Monte_Carlo pulldown 91
- RISM theory for polymer blends 55
- .rst files, see restart files
- run parameter (.mp) files (Mechanical Properties) 321
- running a complete polymorph prediction sequence 134
S
- saving
- Blends interaction energy (.enr) files 45
- Mechanical Property data to file 12
- search level 141, 146
- searching space groups 128, 326
- second derivative method for property prediction 2
- selecting
- frames from trajectory files for Polymer Properties analysis 23
- torsions for dihedral angle distributions in polymers 26
- shear modulus
- not from second derivative 5
- simulated annealing 138
- solutions provided by 160
- theory 160
- solubility parameter 80
- sorbates database 231
- sorption
- energy calculations for 232
- fixed loading simulation 230, 253-254
- fixed pressure simulation 230, 254-256
- Henry constant simulation 230, 256-258
- models for 231, 239
- output 237
- running a simulation 239
- trajectory file analysis 245
- trajectory files 237, 239
- Sorption module 229-258
- sound, velocity of, see velocity of sound
- space group 128, 326
- defining 143
- speed of sound, see velocity of sound
- spinodal curve, see phase diagrams
- Steepest Descent, minimization algorithm 113
- stiffness matrix, methods for calculating 2-4
- strain
- analyzing data in Mechanical Properties 14
- applying in Mechanical Properties 9
- see also stress/strain
- stress
- analyzing data in Mechanical Properties 14
- applying in Mechanical Properties 9
- subrotations, Crystal Packer 106, 123-125
- constraining 112
- defining 124
- sweep
- parameters for mechanical properties calculation 6, 9
- Synthia
- properties calculable 78
T
- 12-10 functional form 122
- table (.dat) files
- output from Mechanical Properties 13
- text
- Mechanical Properties output 12
- sorption output 238, 239
- thermodynamic functions
- calculating for blends 51
- thermodynamic properties 69
- topological information of polymers 85
- torsional energy term, Crystal Packer 123-125
- torsional subrotations, see subrotations
- torsions, see also dihedrals
- trajectory (.trj) files
- for Mechanical Properties 321
- trajectory files, dynamics
- loading for Polymer Properties analysis 22
- selecting frames for Polymer Properties analysis 23
- trajectory files, sorption 237, 239
- analysis of 245
- plotting 245, 249
- transport properties 69
U
- using the Polymorph Predictor 128
V
- valence indices 87
- van der Waals interactions 130
- van Krevelen-like, solubility parameter 80
- VDW energy calculation in sorption 233
- VDW energy term, Crystal Packer 118-120
- VDW radius reduction for bad contacts check 236
- velocity of sound
- equation for 18
- to calculate, see mechanical properties
- Voigt notation for stress/strain tensors 10
- volume compressibility
- equation for 17
- to calculate, see mechanical properties
- Voronoi volume analysis of polymers 36
Y
- Young's modulus
- equation for 17
- to calculate, see mechanical properties
Z
- zeolites database 231
Last updated December 08, 1998 at 07:37PM Pacific Standard Time.
Copyright © 1998, Molecular Simulations, Inc. All rights
reserved.