Contents
Release 4.5, June 2000
How to Use This Book
- Who should use this book
- Things to be familiar with
- Workstation requirements
- How to find information
- Using other Cerius2 books
- Online Documentation
- Typographical conventions
1. Mechanical Properties
- Introduction
- Sections in this chapter
- General methodology
- Second derivative
- Constant-stress minimization
- Default mode
- Custom mode
- Constant strain minimization
- Default and custom mode
- Advantages and drawbacks of the three methods
- Calculating mechanical properties
- Module design
- Novice or expert
- Methods
- Sweep parameters
- Output
- Minimize Model First
- Accumulate Averages
- Data analysis
- Crystal constraints
- Restoring data
- To calculate the mechanical properties of a model
- To determine the effect of crystal constraints
- Specifying the applied stress/strain and mode
- Sweep defaults
- Choosing values
- Choosing the mode
- Applied stress/strain tables
- Standard Voigt notation
- Editing the defaults
- Plot stress/strain profile
- Choosing the mode
- To specify variables for constant-stress minimization
- Sweep Defaults
- Mode
- Stress profile
- Plot profile
- To specify the constant strain minimization variables
- Sweep Defaults
- Mode
- Strain profile
- Plot profile
- Displaying and saving results
- Output variables
- Text and tables files
- Level of detail
- To specify the output variables
- Analyzing the data
- Data plotting
- Data fitting
- To analyze constant-stress minimization data
- Data plotting
- Curve fitting
- Average Y values
- Updating properties
- To analyze constant-strain minimization data
- Restoring data for analysis
- Reload options
- To reload a mechanical properties calculation file
- Theory
- Deriving mechanical properties
- Compliance matrix
- Compressibility
- Bulk modulus
- Young's modulus
- Poisson's ratios
- Velocities of sound
- Lamé constants
- Model, forcefield, and energy setup
- Models
- Force field and energy setup
- References
2. Polymer Properties
- Sections in this chapter
- General Methodology
- Selecting the trajectory file
- To select the trajectory file to be analyzed
- Selecting the trajectory file frames
- To specify the trajectory frames to be analyzed
- Calculating physical and chain properties
- To calculate physical or chain properties
- Select the physical properties
- Select the chain properties
- To analyze the Voronoi volume
- Calculating dihedral distributions
- 1D or 2D plots, time
evolution
- Where variables are set
- Input
- Defining the dihedrals
- To obtain a 1D distribution or 2D plot
- Input the model or trajectory data
- Specify the output
- Define the dihedrals
- Do the calculations
- To plot the time evolution of a single dihedral
- Specifying the torsion selection rules
- Defaults
- To specify the torsion selection rules
- Obtaining orientation function results
- Input
- Where variables are set
- Reference direction
- Structural unit vector
- Information obtained
- To calculate the orientation function and angle distribution
- Input the model or
trajectory data
- Specify the output
- Define the reference direction
- Define the structural unit vector
- Do the calculations
- To plot the time evolution of a single vector
- Specifying the bond selection rules
- Defaults
- To specify the bond selection rules
- To specify a particular bond pair type
- To specify a particular bond order
- To include hydrogen bonds
- Theory
- Physical properties
- Dipole moment
- Quadrupole tensor
- Molecular weight
- Density
- Chain properties -- radius of gyration and end-to-end distance
- Radius of gyration
tensor (S)
- Principal values
and directions
- Radius of gyration (s)
- End-to-end distance (R)
- Voronoi volume analysis
- Voronoi polygon
- Determining Voronoi volume
- Information obtained
- Cutoff distance
- Order versus disorder
- External effects
- Calculating the orientation function (order parameter)
- Defining the terms
- Hermans orientation function, P2
- Order parameter, S
- Average value used, <cos2
>
- Range of values for P2
- Random orientation
- Average angle
3. Blends
- Introduction
- Sections in this chapter
- Utility and applications
- Applications
- Using Blends
- Calculate functions
- Analyze functions
- Extracting pairs
- General methodology
- To calculate pair interaction energies
- Specify the packing
variables
- Specify the calculation controls
- Specify the output
controls
- To calculate a single Eij
- To calculate all Eijs (E11, E12, E21, and E22)
- To calculate the coordination numbers
- Specify the packing
variables
- Specify the calculation controls
- Specify the output
- To calculate a single Z
- To calculate all Zs (Z11, Z12, Z21, and Z22)
- To specify the packing variables
- Specify the alignment
- Specify the noncontact atoms
- To fit the mixing energy data
- To plot the interaction parameter Chi(T)
- To calculate a phase diagram
- Plotting pair energy distributions
- To plot a pair energy distribution
- Plotting thermodynamic functions
- Isotherms
- To calculate and plot thermodynamic functions
- Specify the functions to be computed
- Specify the model
- Specify the degree of polymerization
- Plotting thermodynamic isotherms
- To plot thermodynamic isotherms
- Specify the model
- Specify the degree of polymerization
- Extracting molecular pairs
- To extract molecular pair configurations
- Theory
- Theoretical models
- Flory-Huggins model
- Other theories
- Molecular simulations
- Blends approach
- Extensions to Flory-Huggins model
- Analytical fit
- Information obtained
- Force field employed
- Calculating pair interaction energies
- Sampling problems
- Molecular dynamics
- Blends Monte Carlo sampling technique
- The pairs method
- Packing variables
- Output
- Where variables are set
- Calculating coordination numbers
- Nearest-neighbor
packing
- Packing variables
- Averaged Zijs obtained
- Where variables are set
- Averaged Zs used to
calculate 
- Specifying packing variables
- Isotropic versus axial packing
- Excluded atom constraints
- Fitting the mixing energy and calculating Chi
- Fitting Emix (T)
- Plotting (T)
- Calculating phase diagrams
- Calculating
G
- References
4. Synthia
- Introduction
- Sections in this chapter
- Using Synthia
- A. Building the copolymer
- B. Predicting properties
- C. Studying a range of concentrations
- Summary
- General methodology
- Calculable properties
- Scope and limitations
- Computing repeat unit length
- Energy minimization of repeat units
- Values of cohesive energy and solubility parameter used in correlations for other properties
- Representation of amide groups
- Units of permeability
- Developing correlations with QSAR
- Performing polymer properties calculations
- Theory
- Background
- Connectivity indices of polymer repeat units
- Connectivity indices of polymer chains
- General forms of the correlations in terms of connectivity indices
- Backbone and side group connectivity indices
- Actual correlations for various properties and validation against experimental data
- References
5. RMMC (RIS Metropolis
Monte Carlo)
- Using RMMC
- General Methodology
- RIS Metropolis Monte Carlo (RMMC) Concepts
- Rotatable Bonds
- Energy Calculation
- Parameters Controlling the Simulation
- "RIS" Metropolis Monte Carlo (RMMC) Simulations
- Computing Dihedral Distribution Functions
- Output Files
- Theory
- RIS Metropolis Monte Carlo Simulation
- Properties Calculated with RMMC
- The RMMC Algorithm
- Treatment of Constraints
- References
6. Crystal Packer
- Introduction
- Sections in this chapter
- About Crystal Packer
- Rigid units
- Torsional subrotations
- Quick default
minimization
- General methodology
- Model initialization
- To initialize the model
- To set energy calculation options
- External pressure
- van der Waals preferences
- On-diagonal VDW parameters
- Off-diagonal parameters
- van der Waals interaction range
- Coulomb preferences
- H-bond preferences
- Subrotations
- Defining subrotations
- Fourier parameter sets
- 1-4 interactions
- Minimizer constraints setup
- To set up minimizer constraints
- Variable cell parameters
- Rigid units
- Variable subrotations
- Minimizer preferences setup
- Minimization algorithm
- Modified Newton
- Steepest descents
- Maximum increments
- The contact table
- Updating the table
- Minimization termination
- Energy tolerance
- To set minimization preferences
- Control parameters
- Maximum increments
- Termination criteria
- Calculating energy and running the packing calculation
- To calculate model energy
- To perform a minimization of model energy
- Theory
- Energy expression setup
- The van der Waals term
- Polymer, surface, and
network models
- Treatment of long-range interactions
- Close contact check
- The Lennard-Jones functional form
- On-diagonals
- Off-diagonals
- The Coulomb term
- Minimum charge
- The Ewald sum
- The hydrogen bond term
- Functional form of
H-bond potential
- H-bond parameters
- van der Waals parameters and H-bonds
- The torsional energy term
- The external pressure term
- Uses for external pressure
- References
7. Polymorph Predictor
- Introduction
- Sections in this chapter
- Using the Polymorph Predictor
- Step 1: Setup
- Step 2: Monte Carlo packing simulation
- Step 3: Cluster analysis
- Step 4: Energy minimization
- Step 5: Cluster minimized structures
- Trajectory file merging
- Trajectory file analysis
- Reliability checks
- General Methodology
- Setting up
- Configuring forcefields
- Preparing models
- Minimize and calculate charges
- Flexible molecules
- Simulation parameters
- Predicting Polymorphs
- Polymorph Predictor limitations
- Flexible molecules
- Forcefields
- Processing time
- Intramolecular symmetry
- Running a prediction
- Restarting interrupted prediction procedures
- Defining the molecules in the crystal structure
- To run a complete polymorph prediction sequence
- To predict polymorphs manually
- Monte Carlo packing simulation
- The simulation
- Generating initial
structures
- Heating phase
- Cooling phase
- Trial steps
- Setting Monte Carlo preferences
- Search parameters
- Effects of changing search parameters
- Heating phase
- Cooling phase
- Space groups
- Output options
- Cluster analysis
- Clustering Monte Carlo output
- Clustering energy
minimization output
- Procedure
- Clustering algorithm
- Setting Cluster Analysis preferences
- Input file
- Clustering parameters
- Clustering tolerances for Monte Carlo and minimized output
- Monte Carlo output
- Minimized output
- Identifying sensible clustering values
- Output options
- Energy minimization
- Optimizing the current model
- Setting minimization preferences
- Input file
- Termination criteria
- Rigid Bodies
- Output options
- Notes on rigid body minimization
- Trajectory file analysis and model extraction
- Select trajectory file
- Properties
- Model extraction
- Automatically comparing powder spectra
- Select trajectory file
- Select experimental spectrum
- Transform experimental spectrum
- Specify Diffraction-Crystal settings
- Set CMACS intervals
- Specify an identifier for the comparison
- Calculate measures of comparison
- Analyze measures of comparison
- Show settings
- Delete Set
- To automatically compare powder spectra
- Merging trajectory files
- Reliability checking
- Examine structures/
properties
- Comparison against experimental data
- Symmetry
- Change the FF dielectric parameters
- Theory
- Predicting polymorphs
- Theory
- Effect of disregarding TS
- Reliability checks
- Further reading
- Simulated annealing theory
- Packing simulation difficulties
- Solutions provided by simulated annealing
- Automatically comparing powder spectrad
- References
8. Morphology
- Introduction
- Sections in this chapter
- Using Morphology
- Step 1: Setup
- Step 2: Calculations
- Step 3: Visualization
- Step 4: Listing, editing, adding and removing growth faces
- Step 5: Crystal attributes
- Step 6: Saving the
morphology
- General Methodology
- Applications
- Other Cerius2 modules
- Calculating Morphology with the BFDH method
- Growth planes and growth rate list
- Minimum slice thickness
- Displaying the
morphology
- To calculate morphology with the BFDH method
- Calculating morphology with the Attachment or Surface Energy methods
- Correct molecule
- Listing the growth faces
- Calculating attachment energies
- Slice positioning
- Calculating surface energies
- Deducing the morphology
- Energy setup
- To calculate morphology with the Attachment or Surface Energy methods
- Setting up the energy calculations
- Choosing the force field
- Auto force field switch
- Non bonded energy terms
- Lattice energy and interaction radius
- Saving the energy data
- To set up the energy calculations
- To check the lattice energy
- Slice positioning
- Finding the most stable slice
- Center slice on all
molecules
- Slice offset
- To specify the slice positioning variables
- Editing, adding and removing crystal faces
- Face list
- Selecting faces
- Editing faces
- Adding faces
- Removing faces
- Listing faces
- To edit, add, and remove crystal faces
- Calculating morphology using the Hartman-Perdok Method
- Generating the Crystal Graph
- Generating Connected Nets
- Calculating the Morphology
- Creating a model of a connected net
- Saving the crystal graph and the connected nets
- To calculate morphology with the Hartman-Perdok Method
- Generating and editing the Crystal Graph
- Defining the spatial range
- Generating crystal bonds
- Visualizing crystal bonds
- Editing crystal bonds
- To Generate and edit the Crystal Graph
- Generating and editing Periodic Bond Chains and Connected Nets
- Generating connected nets
- Generating the crystal morphology
- List of connected nets
- Deleting less stable connected nets
- Analyzing connected nets
- Create a model of a connected net
- Display style of a connected net
- Removing dummy atoms
- To Generate and edit Periodic Bond Chains and Connected Nets
- Displaying the morphology
- Visualization
- Scale factor
- Transparency
- Face label
- Redisplay morphology
- To specify the display controls
- Analyzing the morphology
- Interplanar angles and surface areas
- List Areas by Form option
- Aspect ratio
- Cleave selected face
- To analyze the crystal morphology
- Storing morphologies
- Saving
- Loading
- To save the current morphology
- To load a morphology
- Theory
- Bravais Friedel Donnay Harker method
- Growth rates - Bravais Friedel rules
- Growth planes - Donnay Harker rules
- The Attachment Energy method
- Calculating Eatt
- Deducing morphology
- Assumptions
- The Equilibrium Morphology
- Calculating Esurf
- Assumptions
- The Hartman-Perdok method
- Crystal bonds and the crystal graph
- Periodic bond chains (PBCs) and connected nets
- Deducing morphology
- Assumptions
- References
9. Flexisorb
- Introduction
- Using Flexisorb
- Tutorial
- Physi-sorption II - simulating large hydrocarbons
- General Methodology
- Preparing a model
- Selecting a forcefield
- Atom typing
- United-atom versus all-atom
- Calculating energy maps
- Job control
- Calculating gas phase chemical potential
- Using existing map files
- Calculating the isosteric heat
- Predicting the uptake isotherm
- Non-Ideal gases
- Output files
- Analysis
- Creating an isosurface
- Mapping a property onto a surface
- Creating a slice plane
- Displaying a cloud point diagram
- Troubleshooting
- Theory
- General CB-GCMC Acceptance Rules
- Model details
- Forcefield
- Other simulation details
- References
10. Sorption
- Introduction
- Information obtained
- Output forms
- Sections in this chapter
- Using Sorption
- Running a sorption simulation
- General methodology
- Settings for the energy calculation
- Bump checks
- Excluded volumes
- van der Waals radius reduction
- van der Waals energy
- Minimum image convention
- Coulomb energy
- Ewald summation method
- Setting energy calculation options for a sorption simulation
- Forcefield
- Atom types
- Bad contacts
- van der Waals energy
- Coulomb energy
- Using Ewald Grids
- Output during the simulation
- Setting output options for the simulation
- Model window output
- Plotted output
- Trajectory file output
- Snapshot file output
- Text output
- Setting up and running the simulation
- Framework
- Surface
- Surface Setup
- Sorbate
- Move probabilities
- Maximum step sizes
- Rescaling step sizes
- To set up and run the simulation
- Begin the simulation
- Stopping the simulation
- Restarting the simulation
- Analysis of sorption trajectory files
- Trajectory file plots
- Mass distribution plots
- Energy distribution plots
- Loading-curve plots
- Mass cloud plots
- Plotting sorption trajectory files
- Plotting trajectory files
- Plotting mass distribution of sorbates in framework
- Plotting energy distribution of sorbates
- Plotting a loading curve
- Plotting mass clouds (dot density maps) of sorbate positions
- Theory
- Simulation methods
- Fixed loading (canonical ensemble) simulation
- Fixed pressure (grand canonical ensemble) simulation
- Henry's constant simulation
- References
11. MesoDyn
- Sections in this chapter
- Introduction
- Using MesoDyn
- General methodology
- Overview
- Building a molecular ensemble
- Specifying the Run parameters for a MesoDyn simulation
- Setting the host machine and parallel nodes, job monitoring and output handling
- Analyzing the results
- Selecting a system
- Plotting the thermodynamics functions
- Exploring the morphology
- Theory
- Introduction
- Dynamics
- Thermodynamics
- Parameterization: Mapping of the atomistic level to the mesoscale
- Numerics
- References
12. Dissipative Particle Dynamics (DPD)
- Sections in this chapter
- Introduction
- Using DPD
- General methodology
- Building a molecular ensemble
- Specifying the Run parameters for a DPD simulation
- Setting the host machine, job monitoring and output handling
- Analysing the result: Selecting a system, inspecting the files, plotting the thermodynamic functions, and exploring the morphology
- Theory
- Introduction
- Equations of motion for a DPD system
- Integration scheme in DPD
- Choosing the dissipation and random noise magnitudes
- Choosing the repulsion parameters
- Mapping the interactions onto Flory-Huggins theory
- Calculation of Flory-Huggins parameters as input to DPD simulations
- References
A. File Formats
- Mechanical Properties files
- Output files
- File names
- Morphology files
- CIF format
- Interactions.dat
- Polymorph files
- Trajectory file usage and naming
- Tip
B. Using MSI Online Documentation
- MSI Hypertext Locations
LIST OF FIGURES
- Figure 1. Voronoi polygon
- Figure 2. The Repeat Unit (a), and
Corresponding Hydrogen-Suppressed Graph (b)
- Figure 3. The Atomic and Bond Connectivity (a), and Valence (b) Indices for the PVF Repeat Unit
- Figure 4. Nonbond interactions in RMMC energy calculation
- Figure 5. The Cerius2 Visualizer window showing the MESOSCALE card and the main MESODYN menu.
- Figure 6. The MesoDyn Build panels for defining beads, molecules and interactions.
- Figure 7. The MesoDyn Constraints panels for defining regions from which the beads are excluded.
- Figure 8. The MesoDyn Run control panel.
- Figure 9. The MesoDyn Job Control panel.
- Figure 10. The MesoDyn Job Control Options subpanel, with nodes and output paths specified for running on two nodes of a particular IBM sp2.
- Figure 11. The MesoDyn Systems Analysis panel.
- Figure 12. The MesoDyn Thermodynamics panel for plotting the free energy, entropy, and other time-dependent averages.
- Figure 13. The MesoDyn Profiles panels for creating and analyzing slices through the density fields.
- Figure 14. The MesoDyn Isodensities control panel for creating and analyzing isosurfaces of the density fields.
- Figure 15. The Cerius2 Visualizer window showing the MESOSCALE card and the main DPD menu.
- Figure 16. The DPD Build panels for defining beads, molecules, interactions and dissipations.
- Figure 17. The DPD Run panel.
- Figure 18. The DPD bead and molecule Display panels.
- Figure 19. The DPD Job Control panel.
- Figure 20. The DPD System Analysis panel.
- Figure 21. The DPD Plot panel for plotting the bead diffusion coefficients, and polymer endpoint and bond length distributions.
- Figure 22. The DPD Profiles panel for creating and analyzing slices through the density fields.
- Figure 23. The DPD Isodensities panel for creating and analyzing isosurfaces of the density fields.
Last updated December 08, 1998 at 07:18PM Pacific Standard Time.
Copyright © 1998, Molecular Simulations, Inc. All rights
reserved.