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Contents
Adsorption Locator 1
Introduction 1
Further Information 1
Tasks in Adsorption Locator 2
Preparing the structures 2
Optimizing the geometry 3
Assigning charges 4
Defining the adsorption region 4
Finding adsorption sites on a substrate 6
Setting up Adsorption Locator calculations 8
Setting up a simulated annealing run 8
Choosing the energy expression 9
Setting forcefield types 10
Viewing output files 12
Adsorption Locator jobs 14
Using Adsorption Locator job control 14
Live updates 14
Remote Adsorption Locator jobs 14
Adsorption Locator file formats 15
Theory in Adsorption Locator 16
Electrostatic energy 16
Generation of substrate-adsorbate
configurations 16
Metropolis Monte Carlo method 17
Canonical ensemble 18
Simulated annealing 19
Implementation 19
Dialogs in Adsorption Locator 21
Adsorption Locator Calculation dialog 21
Setup tab 21
Energy tab 25
Location tab 30
Properties tab 32
Job Control tab 34
Adsorption Locator References 36
Adsorption Locator
Introduction
Adsorption Locator enables you to simulate a substrate loaded with an adsorbate or an adsorbate
mixture of a fixed composition. Adsorption Locator is designed for the study of individual systems,
allowing you to find low energy adsorption sites on both periodic and nonperiodic substrates or to
investigate the preferential adsorption of mixtures of adsorbate components, for example.
Adsorbates are typically molecular gases or liquids and substrates are usually porous crystals or
surfaces, such as zeolites or carbon nanotubes, or amorphous structures, such as silica gel or activated
carbon. Adsorption Locator identifies possible adsorption configurations by carrying out Monte Carlo
searches of the configurational space of the substrate-adsorbate system as the temperature is slowly
decreased.
Further Information
For more information about the Materials Studio and other BIOVIA software products, visit BIOVIA
Support on the Web: https://community.3dsbiovia.com/
Note: If you do not wish to automatically assign charges at the beginning of each calculation, you
must ensure that Use current is selected from the Charges dropdown list on the Energy tab of the
Adsorption Locator Calculation dialog.
internal voids, segregate the atom volume field using the Create Segregates tool on the
Volume Visualization toolbar.
2. Choose Modules | Adsorption Locator | Calculation from the menu bar to display the Adsorption
Locator Calculation dialog.
3. Select the Location tab.
4. Check the Surface region defined by field values checkbox in the list.
5. Click the Volumetric Selection button on the Volume Visualization toolbar to display the
Volumetric Selection dialog. Use this dialog to select fields and/or field segregates you want to use
for the calculation.
If a single field is chosen, the name of the selected field is displayed, along with the minimum and
maximum mapped (that is, displayed) values of the field. It is these values that will be used to define
the adsorption region, not the global minimum and maximum field values.
Note: If multiple fields are chosen, the adsorption region is defined as the union of all valid field
regions.
6. Click the Edit... button to display the Color Maps dialog. Select the Color Mapping tab and set the
field display range in the From and To fields to define the adsorption region.
Since the energy of the substrate is not calculated in an Adsorption Locator run, there is no
requirement to use Forcite or to use the same energy and minimization settings for the geometry
optimization of the substrate as for the Adsorption Locator run.
Note: For ionic structures, such as metal oxides, the bonds between the metal and the oxygen atoms
are primarily ionic. This means that the concept of a covalent bond is not applicable to these
structures and the bond must be deleted for the calculation to proceed. Conversely, the atoms must
be bonded so that the forcefield typing engine can detect the environment of the atoms to predict
the typing correctly.
In this case, you should use the typing engine to assign forcefield types and charges to the atoms and
then remove the bonds before any calculations are performed. Otherwise, the calculation will look for
bond parameters which do not exist and the calculation will fail.
To assign forcefield types manually
1. Choose Modules | Adsorption Locator | Calculation from the menu bar to display the Adsorption
Locator Calculation dialog.
2. Select the Energy tab.
3. Click the More... button associated with the Forcefield dropdown list to display the Adsorption
Preparation Options dialog.
4. Uncheck the Calculate automatically checkbox.
5. In the active 3D structure document, select the atoms to which you wish to assign the forcefield
types. The default setting assumes all the atoms in the structure have been selected.
6. Choose the forcefield that you wish to assign to the selected atoms from the list of forcefield types.
7. Click the Assign button under Forcefield types.
Tip: Select View | Label from the menu bar to display the Label dialog, which you can use to show the
forcefield types currently assigned to atoms in the structure. Adjust any incorrectly assigned or
unassigned forcefield types by selecting the affected atoms and setting their forcefield types using the
Properties Explorer.
To calculate forcefield types manually
1. Choose Modules | Adsorption Locator | Calculation from the menu bar to display the Adsorption
Locator Calculation dialog.
2. Select the Energy tab.
3. Click the More... button associated with the Forcefield dropdown list to display the Adsorption
Preparation Options dialog.
4. Uncheck the Calculate automatically checkbox.
5. In the active 3D structure document, select the atoms for which you wish to calculate the forcefield
types. The default setting assumes all the atoms in the structure have been selected.
6. Click the Calculate button under Forcefield types.
Live updates
You can monitor important intermediate results during an Adsorption Locator job, for more information
on requesting live updates and their behavior see the main Managing live updates topic.
The Adsorption Job Control Options dialog allows you to control the generation of intermediate
documents and to set the update frequency.
If the Update structure checkbox is checked on the Adsorption Job Control Options dialog, a 3D
Atomistic document ([seedname].xsd) showing the active configuration of the substrate with the
adsorbate molecules is returned. At the end of the job, this document is updated with the lowest energy
configuration found during the run.
If the Update graphs checkbox is checked on the Adsorption Job Control Options dialog, a chart
document ([seedname] Etotal.xcd) showing the evolution of various energy components and the
average total energy over the course of the simulation is returned. If you requested that the energy
density be reported when you set up the simulation (that is, by checking the Energy distribution
checkbox on the Properties tab of the Adsorption Locator Calculation dialog), a chart ([seedname]
Energy.xcd) showing the distribution of intermolecular energy for each adsorbate component is
returned.
If the Update textual results checkbox is checked on the Adsorption Job Control Options dialog,
Materials Studio will display the results document [seedname].txt. Initially, this contains all of the
calculation parameters and is updated if any non-fatal errors occur during the calculation. In addition, a
text file (Status.txt) containing the status of the calculation is returned.
Electrostatic energy
The Ewald & group summation method in Adsorption Locator calculates the electrostatic energy
contribution to ESS and ESF using different methods, again to improve the computational efficiency. The
electrostatic interaction between sorbate molecules is evaluated using charge groups. A charge group is
a small group of atoms that are close to one another and which have a net charge of zero or almost
zero. An electrostatic energy is calculated for each pair of charge groups whose centers are within the
cutoff distance specified when the calculation is set up. Since charge groups are charge neutral, the main
error introduced by using a cutoff distance is due to dipole-dipole interactions. However, such
interactions are usually low energy and act over short distances. Charge groups are defined
automatically by default, but can also be set manually.
Ewald & group summation evaluates the electrostatic interaction between sorbate molecules and the
framework using the Ewald summation method. In the Ewald method, each partial charge on the
sorbate molecule interacts with the entire periodic framework. To evaluate the infinite sum, each partial
charge is screened by a charge distribution of opposite strength. The interaction between two screened
charges is short range and can be evaluated directly; the electrostatic energy contained in the periodic
lattice of charge distributions is evaluated using a Fourier transformation. The accuracy of the Ewald
method largely depends on the width of the screening charge distribution. In Adsorption Locator, the
accuracy of the Ewald method is set as an energy tolerance, from which the width of the screening
charge distribution, as well as the cutoff distance in real and reciprocal space, are derived.
Note: The Ewald & group summation method can only be used when the system, that is, the
framework plus all the sorbate molecules, is overall charge neutral. If there is a net charge on the
system, the Ewald method must be used for summation of both sorbate-sorbate and sorbate-
framework electrostatic interactions.
where C is an arbitrary normalization constant, β is the reciprocal temperature, and E is the total
m
energy of configuration m.
The reciprocal temperature is given by:
where E AA is the intermolecular energy between the adsorbate molecules, E AS is the interaction
m m
energy between the adsorbate molecules and the substrate, and U A is the total intramolecular energy
m
of the sorbate molecules. The intramolecular energy of the substrate is not included as its structure is
fixed throughout the simulation; thus, this energy contribution is fixed and vanishes, since only energy
differences play a role in Adsorption Locator calculations.
The total intramolecular energy, UA, is the sum of the intramolecular energy of all adsorbates of all
components:
Eq. 4
where {N} denotes the set of adsorbate loadings of all components in configuration m.
m
An Adsorption Locator simulation always starts with a clean substrate. The first stage is to adsorb the
specified number of adsorbate molecules of each component. This is accomplished by a random series
of insertion steps and equilibration moves (only moves that do not change the loading are permitted)
until the specified loading has been reached. During this stage, only insertion steps that do not create
structures with intermolecular close contacts and that pass all adsorbate location constraints are
accepted.
Note: The loading stage in Adsorption Locator has a maximum of 100000 insertion steps. If the
specified mixture could not be loaded within this number of insertion steps, the simulation stops and
a loading failure is reported. In this case, you should decrease the number of adsorbate molecules
specified for the simulation.
The starting configuration will take several steps to adjust to the current temperature. A simulation is,
therefore, separated into an equilibration and a production stage. The properties returned at the end of
the run are based on the production stage only.
In the equilibration and production stages of an Adsorption Locator simulation, each step starts with
the selection of a step type using the weights set at the start of the run. The step type can be either a
translation or a rotation. After a step type is selected, a random component is chosen and the step type
is applied to a random adsorbate of that component. The Metropolis Monte Carlo method is then used
to decide whether to accept or reject the change.
In the Metropolis Monte Carlo method, the step that transforms configuration m to n is a two-stage
process. First, a trial configuration is generated with probability α . Then, either the proposed
mn
configuration, n, is accepted with a probability P or the original configuration, m, is retained with a
mn
probability 1 - P . The overall transition probability, π , is thus obtained from:
mn mn
Eq. 6
It is easy to verify by substitution that the following choice for the acceptance probability satisfies Eq. 6.
Eq. 7
This expression can be simplified further. In the traditional Metropolis Monte Carlo method (Metropolis
et al., 1953), trial configurations are generated without bias, that is, α = α . As such, the
mn nm
corresponding acceptance probability (Eq. 7) becomes:
Eq. 8
Thus, transitions of a configuration m to a more likely one (ρ > ρ ) are always accepted, but transitions
n m
to configurations with a lower probability (ρ < ρ ) are less likely to be accepted.
n m
Canonical ensemble
The canonical ensemble is described in Generation of substrate-adsorbate configurations. The
probability of a configuration in this ensemble is given by Eq. 1. Substitution into Eq. 8 leads to the
acceptance probability:
Eq. 9
where β is the reciprocal temperature (Eq. 2) and E is the total energy of configuration m (Eq. 3). In
m
other words, transitions to a configuration of lower energy (E < E ) are always accepted, but transitions
n m
to high energy configurations (E > E ) are only accepted with a probability which decreases
n m
exponentially with the difference in energy to zero. As such, high energy configurations are unlikely to be
sampled, precisely what the probability density of the canonical ensemble (Eq. 1) dictates.
The Metropolis Monte Carlo method in Adsorption Locator provides four step types for a canonical
ensemble: conformer, rotation, translation, and regrowth. A step type is selected at random, using the
weights as specified at the start of the run. The selected step type is applied to a random adsorbate of a
random component as follows:
Simulated annealing
Simulated annealing is a metaheuristic algorithm for locating a good approximation to the global
minimum of a given function in a large search space (Kirkpatrick et al., 1983; Cerný, 1985). The concept is
drawn from the process of annealing in metallurgy, where microcrystalline materials are heated and
then slowly cooled in a controlled manner to increase crystallite size and reduce the number of defects
in the crystal lattice. At high temperatures, the molten material is disordered because the kinetic energy
forces atoms to explore higher energy states, such as substitution or defect sites. The system is cooled
very slowly such that, at any given time, it is approximately in thermodynamic equilibrium. A slow rate
of cooling increases the probability that the atoms will find configurations with lower energy,
corresponding to more regular positions in the crystal lattice. As cooling proceeds, the system becomes
more ordered and finally freezes into a ground state. If the system is not heated to a sufficiently high
temperature or if it is cooled too quickly, lattice defects may become trapped and the system becomes
quenched in metastable states, corresponding to local energy minima.
Any function can be minimized in analogy with this physical process. The object function plays a role
equivalent to the energy of the crystal to be annealed. The function variables correspond to the atom
configurations, with the global minimum solution being the ground state. The algorithm to solve for the
minimum is controlled by a parameter equivalent to the temperature in physical annealing. In order to
minimize the object function, it is evaluated along a sequence of states. At each step, the function is
evaluated for a neighboring state and compared with the current value. If the value has improved, this
replaces the current solution. If the value has worsened, it may still replace the current solution,
depending on how much worse the new solution is within a tolerance set by the control parameter.
Decreasing the control parameter has the effect of reducing the probability that such steps in the
'wrong' direction are accepted. Hence, the above sampling method combined with a slowly decreasing
control parameter provides a way to find a global minimum, starting from an arbitrary initial state.
Implementation
The simulated annealing method uses a canonical Monte Carlo sampling of the search space during
which the temperature is gradually decreased. Each step of the Monte Carlo sampling will attempt to
Setup tab
The Setup tab allows you to choose the quality of calculation that Adsorption Locator will perform and
set the source documents for the adsorbates that are the subjects of the calculation.
Task: Select the type of calculation that you wish to perform from the dropdown list. At present, the
only option available is Simulated annealing.
More...: Provides access to the Adsorption Locator Simulated Annealing Options dialog, which allows
you to set additional parameters associated with the simulated annealing task.
Quality: Set the overall quality for the Adsorption Locator calculation. This setting determines the
parameters that control the simulation speed and accuracy. Available options are:
Note: The document chooser will only show 3D Atomistic documents (.xsd) and 3D Atomistic
Trajectory documents (.xtd). Periodic structures cannot be used as adsorbates for Adsorption
Locator calculations.
Specify the number of adsorbate molecules per cell in the Loading column. The Fraction column
displays the molar fraction corresponding to the specified loading. This column cannot be set directly,
but is automatically updated whenever the Loading values are altered.
Access methods
Energy tab
The Energy tab allows you to select a forcefield to be used in the energy calculation, set the accuracy of
non-bond evaluations, and choose methods for calculating charges and non-bond interactions.
Note: In order to ensure that the energy results returned by Adsorption Locator are accurate, it is
critically important that you use exactly the same energy and minimization settings in the Adsorption
Locator run that you used to optimize the input structures of the adsorbate components. This
includes not only the forcefield, atomic charges, and non-bond summation methods, but also the
quality of the energy and geometry optimization calculations and the convergence tolerances used
for the minimization.
Forcefield: Select a forcefield type from the dropdown list. Available options are:
COMPASS
COMPASSII
Dreiding
Universal
cvff
pcff
Tip: The COMPASS26, COMPASS27, and pcff30 forcefields are no longer automatically available in this
dropdown list. However, these forcefields can be imported into a project from the <MS_
INSTALL>\share\Resources\Simulation\ClassicalEnergy\FORCEFIELDS-LEGACY
directory and then accessed using the Browse... option on the Forcefield dropdown list.
See Installing Materials Studio for details of the <MS_INSTALL> location.
In addition to the standard forcefields, the above list can be supplemented with custom forcefields.
Custom forcefields are added by selecting Browse... from the bottom of the Forcefield dropdown list
and this will display the Choose Forcefield dialog that will allow you to add custom forcefields to the list.
Note: The COMPASS forcefield and its variants are part of the separately licensed module COMPASS.
If you want to use COMPASS with this module, you will need to purchase it separately.
More...: Provides access to the Adsorption Preparation Options dialog, which contains further options
for preparing a structure for a calculation, in particular, assigning forcefield types and bond orders.
Note: The Quality setting here propagates from the overall quality level selected for the calculation
on the Setup tab. As a result, altering the Quality setting here will cause the overall quality of the
calculation to be displayed as Customized.
Electrostatic: Select the summation method to be used for electrostatic interactions from the dropdown
list. Available options are:
Atom based
Group based
Ewald
Ewald & Group
Note: The Ewald and Ewald & Group options for electrostatic interactions are only available when a
periodic structure is in scope.
van der Waals: Select the summation method to be used for van der Waals interactions from the
dropdown list. Available options are:
Atom based
Group based
More...: Provides access to the Adsorption Non-Bond Options dialog, which contains further options for
setting parameters for non-bond interactions.
Access methods
Forcefield types
The Forcefield types list shows the names and brief descriptions of available forcefield types. Click on the
column headings of the list to change the sorting in the columns.
Calculate automatically: When checked, indicates that forcefield types will be calculated automatically
at the start of the simulation. Default = checked.
Occasionally, the forcefield types calculated automatically are inappropriate. Forcefield types can be
applied manually using the Assign button or the Properties Explorer. However, under normal
circumstances, manual assignment is not required and, for large systems, this can be a time-consuming
task.
When the automatic assignment fails, it is necessary to assign forcefield types manually. In such cases,
you should first prevent automatic typing by unchecking the Calculate automatically checkbox, then
selecting the appropriate forcefield type, and finally clicking the Assign button to apply forcefield types
to the system.
Note: When you are using the COMPASSII, COMPASS, pcff, or cvff forcefield the correct formal
charges should be assigned in order for the correct forcefield types to be assigned.
This is especially important for metals, metal halides, and metal oxides atoms where the automatic
assignment may not be appropriate. If you are unsure review the Description of the Forcefield type
on the Preparation Options dialog for the current module.
Note: For ionic structures, such as metal oxides, the bonds between the metal and the oxygen atoms
are primarily ionic. This means that the concept of a covalent bond is not applicable to these
structures and the bond must be deleted for the calculation to proceed. Conversely, the atoms must
be bonded so that the forcefield typing engine can detect the environment of the atoms to predict
the typing correctly.
In this case, you should use the typing engine to assign forcefield types and charges to the atoms and
then remove the bonds before any calculations are performed. Otherwise, the calculation will look for
bond parameters which do not exist and the calculation will fail.
Calculate: Computes forcefield types for the selected molecular fragment. This is useful for systems that
have already been prepared and have subsequently been extended, for example, one or more
molecules have been added. As long as no bonds have been made to the original system, the new
substructure can be selected and then the forcefield types calculated (or assigned) without affecting the
original structure.
Tip: The Cutoff distance and Ewald accuracy parameters can also be set using the preset Quality
settings on the Energy tab. Four quality levels are available: Coarse, Medium, Fine, and Ultra-fine. The
values associated with these quality levels are listed in the table below.
Location tab
The Location tab allows you to specify the region around the substrate in which adsorbate
configurations will be sampled.
A list of region definition options is displayed at the top of the dialog. Select the method you wish to use
to define the adsorption region by checking the appropriate checkbox in the list. Once you select a
location checkbox, additional options are displayed below the list.
Access methods
Access methods
Access methods
Menu Modules | Adsorption Locator | Calculation | Location | Surface region defined by atom set
Toolbar | Calculation | Location | Surface region defined by atom set
Menu Modules | Adsorption Locator | Calculation | Location | Surface region defined by field
values
Toolbar | Calculation | Location | Surface region defined by field values
Properties tab
The Properties tab allows you to select the properties that will be computed as part of the Adsorption
Locator calculation.
Choose the properties you wish to compute by checking the appropriate checkboxes in the list. Once
you select a properties checkbox, additional options are displayed below the list.
Note: The Density field and Energy field options are visible only when the currently active document
contains a 3D periodic structure.
Access methods