Adsorption Locator Guide: Materials Studio 2017

ADSORPTION LOCATOR GUIDE
MATERIALS STUDIO 2017

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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/
Page 1 | Materials Studio • Adsorption Locator Guide

Tasks in Adsorption Locator
Adsorption Locator enables you to simulate a pure adsorbate (or a mixture of adsorbate components)
adsorbed on a substrate. 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.
At present, Adsorption Locator offers a single task:
Simulated annealing: Simulates a substrate loaded with an adsorbate or an adsorbate mixture of a fixed
composition. A low energy adsorption site is identified by carrying out a Monte Carlo search of the
configurational space of the substrate-adsorbate system as the temperature is slowly decreased. This
process is repeated to identify further local energy minima.
To select an Adsorption Locator task
1. Choose Modules | Adsorption Locator | Calculation from the menu bar to display the Adsorption
Locator Calculation dialog.
2. Select the Setup tab.
3. Select the required Adsorption Locator task from the Task dropdown list.
Preparing the structures

The main inputs to an Adsorption Locator run are a 3D Atomistic document containing the structure of
the substrate and either 3D Atomistic documents or 3D Atomistic Trajectory documents containing the
adsorbate components.
The substrate can either be a nonperiodic structure or a periodic structure with primitive (P1) symmetry.
Higher symmetry can be removed by converting to P1 symmetry. If necessary, you can expand the unit
cell by creating a crystal supercell. If you wish to use an adsorbent surface, you should first construct a
surface model and then build a crystal slab from this surface.
The adsorbate components must have a nonperiodic structure. Atom positions must not be fixed.
Adsorbate structures can be input as trajectories of conformations; trajectory documents can be
generated using classical simulations tools.
Note: When using a trajectory of conformations for an adsorbate structure, it is recommended that
you generate the trajectory using a simulation of a single molecule using the same energy settings as
you intend to use in the Adsorption Locator calculation.
In order to ensure that the energy results returned by Adsorption Locator are accurate, it is critically
important that you perform geometry optimizations of the adsorbate structures using the same energy
and minimization settings as you intend to use for your Adsorption Locator run. 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. You
should also ensure that the substrate structure is plausible under the conditions to be used in
Adsorption Locator.
Note: The substrate structure is always held fixed and the intramolecular energy of the substrate is
never evaluated in Adsorption Locator. It is, therefore, possible to obtain meaningful results with
Adsorption Locator even if the selected forcefield is not optimized to describe the substrate structure.
Tasks in Adsorption Locator | Page 2

To prepare the input structures
1. Either import the structures of the adsorbate components from pre-existing files or construct new
molecules using the sketching tools in the Materials Visualizer.
2. Select an energy expression. This process should include the assignment of appropriate charges to
the atoms in the structures.
3. Perform geometry optimizations of the adsorbate structures. Ensure that not only the energy
expression selected in the previous step, but also the quality settings for the energy and geometry
optimization calculations and the convergence tolerances for the minimization that you intend to
use for the Adsorption Locator run are also used for the adsorbate geometry optimizations.
4. Check that the optimized geometries are chemically plausible or compare them with available
experimental data and/or the results of quantum mechanical calculations. If necessary, modify the
energy expression (forcefield, charges, energy settings) to obtain better agreement.
5. Optimize the geometry of the substrate and verify that it is chemically plausible. Since the energy of
the substrate is not calculated in an Adsorption Locator run, there is no requirement to use the
same energy and minimization settings for this calculation as for the Adsorption Locator run.
Optimizing the geometry
Before performing an Adsorption Locator calculation, it is important that you optimize the geometry of
the input structures. You must use Forcite to minimize the structures of the adsorbate components.
Select an appropriate energy expression and verify that it is able to calculate the geometries and
potential energy surfaces of the adsorbate components with a high degree of accuracy. In addition to
this energy expression, you must also use the quality settings for the energy and geometry optimization
calculations and the convergence tolerances for the minimization that you intend to use for the
subsequent Adsorption Locator run.
To optimize an input structure using Forcite
1. Make the 3D Atomistic document containing the input structure the active document.
2. Choose Modules | Forcite | Calculation from the menu bar to display the Forcite Calculation dialog.
3. Select the Setup tab.
4. Select Geometry Optimization from the Task dropdown list.
5. Click the More... button to display the Forcite Geometry Optimization dialog.
6. When minimizing the adsorbate components, specify the same geometry optimization settings as
you intend to use for the Adsorption Locator calculation, including the convergence tolerances and
the minimization Quality setting. For the substrate, specify appropriate geometry optimization
settings and ensure that the Optimize cell checkbox is checked.
7. Select the same energy settings as you intend to use for the Adsorption Locator calculation,
including the Quality setting for the energy calculation, and assign appropriate charges.
8. Click Run to perform the geometry optimization.
Note: Adsorption Locator uses the Forcite classical simulation engine to evaluate the energy
expression and provides the same functionality as Forcite. In order to ensure that the energy results
returned by Adsorption Locator are accurate, it is critically important that when you use Forcite to
optimize the structures of the adsorbate components, you use the same energy and minimization
settings as you intend to use for your Adsorption Locator run. 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.

Assigning charges
A forcefield charge is simply a value that the forcefield suggests as the partial charge of an atom. Not all
forcefields have charges associated with them and the overall neutrality of a structure is not always
guaranteed. When a forcefield supports charges, they will be, by default, assigned automatically at the
same time as the forcefield types are assigned. You may, however, prefer to assign charges manually.
It is important to assign the correct charge as electrostatic interactions play a critical role in determining
the structures of and interactions between organic molecules.
A number of forcefields supplied with Materials Studio, such as COMPASS, cvff, and pcff, have been
parameterized with non-zero forcefield charges and employ the bond increments approach. When using
these forcefields, you would normally accept the default option to use Forcefield assigned charges,
instead of assigning specific charges.
On the other hand, the Dreiding and Universal forcefields do not contain a specific charge model. In
these cases, it is usually preferable to use charges derived from the electrostatic potential obtained from
high quality quantum mechanical calculations using, for example, DMol3 or VAMP (so-called ESP-fitted
charges). If such calculations are not available, Materials Studio provides alternative, though less
accurate, methods with which to calculate charges.
Forcefield charges can also be obtained from molecular data files such as an .msi or .mdf file. These
structure files are usually created by modeling programs such as Cerius2, Insight II, or QUANTA. Charges
are also stored in Materials Studio structure files (.xsd). Structures that have been assigned charges
and then saved in one of these formats do not need to be recharged, unless they have been modified.
Tip: To view the currently assigned charges, use the Label dialog to label atoms by charge.
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.
Defining the adsorption region

Adsorption Locator provides three different approaches to defining the region of the substrate that is to
be searched for low energy adsorption sites:
You can define a volume surrounding the entire substrate within which the adsorbate components can
be added. For periodic structures, the bounding box is the unit cell. For nonperiodic substrates, the
bounding box is drawn as a cuboid, such that the distance between the outermost atoms of the
substrate and the bounding box is always equal to or less than the specified maximum adsorption
distance.
Alternatively, you can specify a subset of the atoms in the substrate structure and restrict the search to
a region around these target atoms. The atoms are defined by creating an atom set entitled
TargetAtoms and the search region is then defined such that the distance between each of the target
atoms is always equal to or less than the specified maximum adsorption distance.
Finally, you can use fields to define the adsorption region. Here, the search region is defined by the
volume of the displayed fields. The adsorption volume can be adjusted by changing the display range of
the fields.

To define the adsorption region using a bounding box
1. Ensure that the 3D Atomistic document containing the substrate structure is the active document.
3. Select the Location tab.
4. Check the Bounding box checkbox in the list.
5. For nonperiodic substrates, you can specify the maximum distance between the bounding box and
the substrate by checking the Set maximum adsorption distance checkbox and specifying a
distance, in Å, in the associated text box.
Note: If you do not specify a value for the maximum adsorption distance, Adsorption Locator will use
a reasonable default value.
The maximum adsorption distance cannot be specified for periodic substrates. The bounding box for
a periodic system is always the unit cell.
To define the adsorption region using a target atoms set
1. Ensure that the 3D Atomistic document containing the substrate structure is the active document.
4. Check the Surface region defined by atom set checkbox in the list.
5. If a set of atoms entitled TargetAtoms has already been defined for the active 3D Atomistic
document, click the Select atoms in TargetAtoms set button to select the atoms in the set. If you do
not wish to use the existing set in your calculation, you will need to delete or rename it using the Edit
Sets dialog or the Properties Explorer, respectively.
6. To define a target atoms set, select the substrate atoms to be included in the set from the active 3D
Atomistic document and click the Add selected atoms to TargetAtoms set button. If a set of atoms
entitled TargetAtoms has already been defined for the active 3D Atomistic document, any of the
selected atoms that are not already members of the set will be added to it.
Tip: You can also create a target atoms set using the Define New Set dialog, but you should
ensure that you name the set TargetAtoms; otherwise, Adsorption Locator will not recognize it.
7. If you wish to specify the maximum distance between the target atoms and the substrate, check the
Set maximum adsorption distance checkbox and specify a distance, in Å, in the associated text box.
Note: If you do not specify a value for the maximum adsorption distance, Adsorption Locator will use
a reasonable default value.

To define the adsorption region using fields or field segregates
1. Ensure that the 3D Atomistic document containing the substrate structure and the required field is
the active document. Volumetric fields are output by many Materials Studio applications and you
can use the Atom Volumes & Surfaces tool in the Materials Visualizer to create an atom volumes
field without a simulation. To generate fields corresponding to accessible or inaccessible regions of
internal voids, segregate the atom volume field using the Create Segregates tool on the
Volume Visualization toolbar.
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.
Finding adsorption sites on a substrate

The Simulated annealing task in Adsorption Locator simulates a substrate loaded with an adsorbate or
an adsorbate mixture of a fixed composition. A low energy adsorption site is identified by carrying out a
Monte Carlo search of the configurational space of the substrate-adsorbate system as the temperature
is slowly decreased. This process is repeated to identify further local energy minima.
During the course of the simulation, adsorbate molecules are randomly rotated and translated around
the substrate. The configuration that results from one of these steps is accepted or rejected according
to the selection rules of the Metropolis Monte Carlo method.
To find adsorption sites on a substrate
1. Either import the structures of the adsorbate components from pre-existing files or construct new
molecules using the sketching tools in the Materials Visualizer. To be used in Adsorption Locator,
adsorbate structures must be molecular. Periodic adsorbate components cannot be used.
2. The substrate can either be nonperiodic or periodic. If available, import the structure of the
substrate. Otherwise, nonperiodic substrates can be constructed using the sketching tools and
periodic substrates can be prepared using the tools for building crystals, surfaces, and
nanostructures in the Materials Visualizer.
3. Prepare the structures of the substrate and the adsorbate components, ensuring that if the
substrate structure is periodic, higher symmetry is removed by converting to P1 symmetry.
4. Optimize the structures, select an appropriate energy expression, and check the forcefield settings.
If you wish to input any adsorbate components as a collection of conformations, use a classical
simulations tool such as Forcite to generate a trajectory file.

Note: You must use Forcite to minimize the structures of the adsorbate components. In order to
ensure that the energy results returned by Adsorption Locator are accurate, it is critically
important that when you optimize the structures, you use the same energy and minimization
settings as you intend to use for your Adsorption Locator run. 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.
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: When using a trajectory of conformations for an adsorbate structure, it is recommended

that you generate the trajectory using a simulation of a single molecule using the same energy
settings as you intend to use in the Adsorption Locator calculation.
5. If you wish to use a field to define the adsorption region around the substrate, generate an atom
volume field using the Atom Volumes & Surfaces tool.
6. Make the 3D Atomistic document containing the substrate structure the active document.
8. Select the Setup tab and set the Quality of the calculation.
9. If you wish to customize any of the job settings, click the More... button to display the Adsorption
Locator Simulated Annealing Options dialog and alter the parameters accordingly.
10. If you wish to modify any of the minimization parameters, click the More... button on the
Adsorption Locator Simulated Annealing Options dialog to display the Adsorption Geometry
Optimization dialog and adjust the settings as required.
11. In the Adsorbates table, complete a row for each structure to be used in the calculation.
a. Choose an Adsorbate from the dropdown list.
b. Specify the Loading or the Fraction with respect to other components.
c. To remove an adsorbate, select the row and press the DELETE key.
12. Choose the Energy tab. Select the appropriate Forcefield and Charges for your input structures as
determined in step 4. If you wish to modify the energy expression parameters, click the More...
button to display the Adsorption Preparation Options dialog and alter the settings accordingly.
13. Select summation methods to be used for Electrostatic and van der Waals interactions. If you wish
to modify the non-bond interaction parameters, click the More... button to display the Adsorption
Non-Bond Options dialog and alter the settings accordingly.
14. Select the Location tab. Check the appropriate checkbox in the list to select a region definition
option and define the adsorption region around the substrate.
15. Select the Properties tab. If you wish to compute any additional properties of the system as part of
the Adsorption Locator run, check the appropriate checkboxes in the list and set the associated
parameters as required.
16. Select the Job Control tab and choose a server on which to run the Adsorption Locator job from the
Gateway location dropdown list. If necessary, specify the Queue to which the job will be submitted.
Adsorption Locator will automatically assign a name to the job based on the name of the 3D
Atomistic document containing the substrate. If you wish to specify an alternative name, uncheck
the Automatic checkbox and enter the new name in the Job description text box.

17. Click the More... button to display the Adsorption Job Control Options dialog. Select the documents
to be used for live updates and set the behavior of Adsorption Locator on job completion.
18. Click the Run button.
19. If you wish, you can examine the intermediate results to ensure that the calculation parameters are
reasonable.
20. After the job has finished, view the output files.
The results of the simulation are presented in a study table document. There is one row for each low
energy configuration found. If you requested that the structures of the low energy configurations be
returned when you set up the simulation (that is, by checking the Low energy configurations checkbox
on the Properties tab of the Adsorption Locator Calculation dialog), Adsorption Locator will include
structure documents in the first column of the study table. In addition to the study table, Adsorption
Locator also returns two chart documents showing the evolution of various energy values over the
course of the simulation and a 3D Atomistic document containing the lowest energy configuration of the
substrate with the adsorbate molecules found during the run.
If you requested that fields be created when you set up the simulation (that is, by checking the Density
field and/or Energy field checkboxes on the Properties tab of the Adsorption Locator Calculation dialog),
they are returned with the substrate structure in a second 3D Atomistic document.
Setting up Adsorption Locator calculations

The process of setting up an Adsorption Locator calculation involves the following steps:
Make the 3D Atomistic document containing the substrate the active document
Specify the 3D structure documents containing the nonperiodic adsorbate components
Select an energy expression and associated parameters appropriate for the structures being studied
Select any additional properties of the system that are to be computed as part of the Adsorption
Locator run
Specify a server gateway to use for the calculation
In addition, you can specify:
How you want to follow the progress during an Adsorption Locator simulation
Whether to open an output document on completion
Setting up a simulated annealing run
The Simulated annealing task in Adsorption Locator allows you to simulate a substrate loaded with a set
number of adsorbate molecules. Low energy adsorption sites are identified by repeatedly searching the
configurational space of the substrate-adsorbate system as the temperature is slowly decreased and
then reset to the maximum through a number of temperature cycles. Adsorbate molecules are confined
to a defined adsorption region in the vicinity of the substrate such that the number of adsorbate
molecules on the surface does not change. The adsorbate is typically a gas or a liquid and the substrate
is usually a porous crystal or surface, such as a zeolite or a carbon nanotube, or an amorphous
structure, such as silica gel or activated carbon.
Adsorption Locator uses the Metropolis Monte Carlo method to search for adsorption configurations.
In this method, only the positions and orientations of the sorbate molecules are sampled; each
conformation is treated as a rigid body. The Metropolis method assumes that the adsorbate molecules
do not have a high degree of torsional flexibility and ignores any internal degrees of freedom that the
adsorbate components may possess on the substrate surface.

Geometry optimization
When Adsorption Locator finds a low energy conformation, the structures of the adsorbate
components are minimized until they satisfy certain specified criteria. This geometry optimization is
carried out using an iterative process in which the atomic coordinates are adjusted until the total energy
of a structure is minimized, that is, it corresponds to a local minimum in the potential energy surface.
Geometry optimization in Adsorption Locator is based on reducing the magnitude of calculated forces
until they become smaller than defined convergence tolerances. The forces on an atom are calculated
from the potential energy expression and will, therefore, depend on the forcefield that is selected.
Adsorption Locator offers a number of algorithms for geometry optimization:
Steepest descent
Conjugate gradient (Polak-Ribiere variant only)
Quasi-Newton (BFGS variant only)
ABNR (Adjusted basis set Newton-Raphson)
Smart
Different algorithms are better suited to certain circumstances, for example if the structure is far from
equilibrium, it is best to use steepest descent. It is, therefore, often beneficial to combine algorithms in a
cascade, such that, as the potential minimum is approached, a more appropriate method is used. The
Smart algorithm is a cascade of the steepest descent, ABNR, and quasi-Newton methods.
Choosing the energy expression
Adsorption Locator simulates adsorption using forcefield technology. In order for a calculation to be
successful, it is important to select an energy expression that is able to accurately describe all the
structures in the calculation and the influence of intermolecular interactions on these molecules.
Adsorption Locator provides a number of different forcefields, each optimized for different elements and
structure types. Further details are given in the Classical simulations theory section. You should use a
forcefield that works well for the atom types (that is, the elements and their hybridization) in the
structure. The Dreiding forcefield is a good starting point as it models carbon, nitrogen, oxygen, and
hydrogen most accurately. However, the Dreiding forcefield models sulfur, phosphorus, chlorine, and
bromine less accurately, and so on down the periodic table, and does not work well for molecules
containing metals.
The correct description of electrostatic interactions is important for an accurate energy expression.
During the preparation of the input structures for an Adsorption Locator calculation, appropriate partial
charges should be assigned to all atoms in the molecule.
Four different summation methods are available for electrostatic interactions in Adsorption Locator:
atom-based, group-based, Ewald, and Ewald & group (where interactions between charge groups are
calculated using group-based summation, while all other interactions are calculated using Ewald
summation). Adsorption Locator gives you the option of using either atom-based or group-based
summation methods for van der Waals interactions.

To choose an energy expression
2. Select the Energy tab.
3. Select a forcefield from the Forcefield dropdown list.
4. Adsorption Locator allows you to charge the input structure automatically before commencing any
energy calculations. It is recommended that you use the default values. For forcefields that include
their own charges, the default is to use those Forcefield assigned charges. For all other forcefields,
the default is to Use current charges assigned to the input structures. In these cases, you must
ensure that charges have been assigned to the input molecules. Applying the Use current option
consistently ensures that exactly the same charges are used for all Adsorption Locator runs and that
they are the same as those used for the initial preparation of the structures.
5. Choose the accuracy of energy expression evaluation from the Quality dropdown list. By default, the
quality level set here will correspond to the overall Quality selected for the calculation on the Setup
tab.
6. Select a summation method for the Electrostatic and van der Waals interactions.
7. Click the More... button to display the Adsorption Non-Bond Options dialog.
8. Optionally, modify the parameters of the summation methods selected for the electrostatic, van der
Waals, and (if contained by the forcefield) hydrogen-bonded interactions by selecting the
appropriate interaction from the list at the top of the dialog and entering the required values in the
available fields.
9. By default, Adsorption Locator automatically assigns forcefield types. If you wish, you can override
this behavior and modify the forcefield types manually.
Note: In order to ensure that the energy results returned by Adsorption Locator are accurate, it is
critically important that once you have identified a suitable energy expression, you use exactly the
same energy and minimization settings in the Adsorption Locator run that you use 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.
Setting forcefield types

Forcefield types are assigned by applying a set of rules that will test for such things as the element type
of the atom, its hybridization, the other elements to which it is bound, and so on. The exact details by
which forcefield types are assigned depend on the forcefield used for the calculation. The forcefield
typing process must be completed before an energy can be evaluated.
To use a custom forcefield, select Browse... from the Forcefield dropdown list on the Energy tab of the
Adsorption Locator Calculation dialog to open the Choose Forcefield dialog and select the desired
custom forcefield from the project.
By default, Adsorption Locator will automatically assign forcefield types before a calculation is
performed. Forcefield types can also be assigned or calculated manually using the Adsorption
Preparation Options dialog, which can be accessed from the Energy tab of the Adsorption Locator
Calculation dialog.

Note: Occasionally, a particular forcefield type assigned using the automatic typing rules may be
inappropriate. In such cases, the particular forcefield type may be altered directly using the
Adsorption Preparation Options dialog (or the Properties Explorer). If forcefield types are assigned in
this way, it is important that the Calculate automatically checkbox is left unchecked to prevent any
subsequent retyping.
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
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
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.

critically important that once you have identified a suitable forcefield, you use exactly the same
energy and minimization settings in the Adsorption Locator run that you use 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.
Viewing output files

Running an Adsorption Locator job produces a number of output files which can be viewed as text,
charts, or study tables.
The main textual output of an Adsorption Locator run is the report document <seedname>.txt, which
contains the settings used and a summary of the main results.
The main structural output of an Adsorption Locator run is a 3D Atomistic document <seedname>.xsd,
this is the lowest energy configuration of the substrate with the adsorbate molecules found over the
course of the simulation.
The results of an Adsorption Locator run are also reported in a study table document
<seedname>.std. The study table lists a variety of energy values for the configurations sampled in the
simulation, which are ordered by total energy.
If you requested the simulation to return the structures of the low energy configurations (by checking
the Low energy configurations checkbox on the Properties tab of the Adsorption Locator Calculation
dialog), these structure documents will be in the first column of the study table. If you requested that
the structures of the adsorbate components and the substrate for comparison purposes (by checking
the Include original substrate and adsorbate(s) in study table checkbox when Low energy
configurations is selected on the Properties tab), these structure documents will be in separate rows in
the output study table.
If you requested fields when you set up the simulation (by checking the Energy field and/or Density field
checkboxes on the Properties tab of the Adsorption Locator Calculation dialog), then a 3D Atomistic
document (<seedname> Fields.xsd) containing the substrate with the requested field data is
generated.
Adsorption Locator study table documents
The Adsorption Locator study table document provides energetic details of the configurations, as
calculated during the run. It may also contain structure documents showing the adsorption positions of
the adsorbate components on the substrate.
The study table infrastructure provides extensive functionality for sorting, filtering, processing, and
plotting these data. It also allows you to calculate additional properties.
The Adsorption Locator study table output can contain some or all of the following columns:

Structure: The configurations of the adsorbate components on the substrate.
Total energy: The total energy, in kcal mol-1, of the substrate-adsorbate configuration. This is the
sum of the energies of the adsorbate components, the rigid adsorption energy, and the deformation
energy. The substrate energy is taken as zero.
Adsorption energy: The energy, in kcal mol-1, released (or required) when the relaxed adsorbate
components are adsorbed on the substrate. This is the sum of the rigid adsorption energy and the
deformation energy for the adsorbate components.
Rigid adsorption energy: The energy, in kcal mol-1, released (or required) when the unrelaxed
adsorbate components (before the geometry optimization step) are adsorbed on the substrate.
Deformation energy: The energy, in kcal mol-1, released when the adsorbed adsorbate components
are relaxed on the substrate surface.
dEad/dNi: The energy, in kcal mol-1, of substrate-adsorbate configurations where one of the
adsorbate components has been removed.
Adsorption Locator chart documents
Some charts are generated by Adsorption Locator simulations: <seedname> Energy.xcd contains the
energy distribution of the sorbate and <seedname> Etotal.xcd contains the evolution of the total,
van der Waals, electrostatic, intramolecular, and average total energy of the entire system of the course
of the calculation.
Adsorption Locator report files
The first section of an Adsorption Locator report file contains all the settings used as input for the
calculation. The second section provides a short summary of the calculation results.

Adsorption Locator jobs
This section covers requesting Adsorption Locator live updates and controlling and running remote
Adsorption Locator jobs.
Using Adsorption Locator job control

Materials Studio can run Adsorption Locator jobs as background processes on a server. The following
tools are provided to setup and control the jobs:
Use the Job Control tab on the Adsorption Locator Calculation dialog to select the gateway location
and job parameters for future jobs.
Use the Server Console application to add new servers and to monitor multiple jobs.
Use the Job Explorer to monitor multiple jobs.
For further information on using job control see the main job control topic.
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.
Remote Adsorption Locator jobs

Adsorption Locator uses a client-server architecture that allows you to use your PC to control
calculations running on a remote computer.
This separation of the client user interface from the server system, where the actual calculation is run,
allows you to use a high performance supercomputer to carry out calculations from your Windows
desktop PC. It also allows you to make use of spare CPU cycles on other desktop PCs.
Adsorption Locator jobs are controlled by input files that are generated by Materials Studio when you
start a job. Adsorption Locator writes the results of the calculations to various output files, which are
downloaded from the server to the appropriate Materials Studio project when the job is completed.
Adsorption Locator jobs | Page 14

Adsorption Locator remote jobs run according to the standard sequence of processes described in A
sample remote job run.
For generic reasons for remote job failures please consult the If a remote job fails help topic. In most
cases, the error message is reported in the Adsorption Locator report file [seedname].txt or in the
MatStudioLog.htm file located in the server-side project directory [seedname]_Files.
Adsorption Locator file formats

The Adsorption Locator server uses native Materials Studio documents for all input, output, and file
settings.
The execution of the Adsorption Locator job is driven by a Perl script that is generated by Materials
Studio when the job is submitted. During the execution of the job on the server, Adsorption Locator
creates a Materials Studio project, [seedname].stp, in a server-side job folder. This project contains
all of the input files and settings that define the Adsorption Locator job. All output documents are
written to the project documents folder on the server, [seedname]_Files/Documents. After the job
is completed, the entire contents of the project documents folder are downloaded into the job results
folder on the client.
Note: If, for any reason, Materials Studio fails to download the results of an Adsorption Locator job,
you may transfer the documents back to your PC. To do this, copy and paste or FTP all files and
subfolders in the server-side [seedname]_Files/Documents folder to the main client-side job
results folder.
The table below summarizes information on the format and purpose of all the major file types. All
locations are relative to the server-side project documents folder, [seedname]_Files/Documents.
File type Input or Brief description

output
[ Input / Structure document containing the substrate that is the subject of the
seedname Output calculations.
].xsd
Status.txt Output Text document containing details of the calculation.
[ Output Text document containing a summary of the job results.
seedname
].txt
[ Output Study table document containing results in tabular format.
seedname
].std
[seedname] Output Folder used to store any structure documents embedded in the study
Files* table.
.xcd Output Chart documents containing results in graphical format. These charts are
also used to display live updates.
* These files are hidden by default, so they will not appear in the Materials Studio Project Explorer; these
files are only visible in Windows Explorer if Windows on your machine is configured to show hidden files.

Theory in Adsorption Locator
Adsorption Locator simulates a substrate loaded with an adsorbate or an adsorbate mixture of a fixed
composition, 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.
Possible adsorption configurations are identified by carrying out Monte Carlo searches of the
configurational space of the substrate-adsorbate system as the temperature is slowly decreased
according to a simulated annealing schedule.
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.
Generation of substrate-adsorbate configurations

In an Adsorption Locator simulation, the candidate substrate-adsorbate configurations are sampled
from a canonical ensemble. In the canonical ensemble, the loading of all adsorbate components on the
substrate, as well as the temperature, are fixed.
The probability of a configuration, m, in the canonical ensemble is given by (for example, Frenkel and
Smit, 2002):
Eq. 1
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:
Theory in Adsorption Locator | Page 16

Eq. 2
where k is the Boltzmann constant and T is the absolute temperature.

B
The total energy of configuration m is calculated according to the following sum:
Eq. 3
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.
Metropolis Monte Carlo method

Experimentally, a molecular system is described by a small number of parameters, such as volume and
temperature. The collection of molecular configurations that satisfy this partial knowledge is called an
ensemble of configurations. An ensemble is described by a distribution function, ρ , that represents the
m
probability of each configuration, m, in the ensemble, for example Eq. 1 for the canonical ensemble.

The Metropolis Monte Carlo method used in Adsorption Locator samples the configurations in an
ensemble by generating a chain of configurations, m, n, ..., where the probability of transition from m to
n is π . Thus, if configuration m is sampled with a frequency ρ , then, on average, ρ π of them are
mn m m mn
transformed to n. Likewise, ρ π of configurations n are transformed to m. Clearly, these fluxes must
n nm
be the same to preserve the density, ρ, otherwise, there would be a net flow from m to n (or vice versa)
and this would increase ρ (or ρ ) and a different ensemble would be sampled. Thus, the following
n m
detailed balance condition for equilibrium is obtained:
Eq. 5
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:

Conformer
The conformation of the selected adsorbate is replaced with a randomly chosen conformation from
the trajectory for that species. The new conformer is given the position and orientation of the old
conformer. If a trajectory of conformations has not been supplied for the selected adsorbate
component (or the trajectory document contains only one frame) a conformer swap will not be
attempted.
Rotation
The selected adsorbate is rotated about its center of geometry by an angle of δθ about an axis, A. The
rotation δθ is drawn from a uniform distribution between -Δ and Δ , where Δ is the maximum
r r r
rotation amplitude. The axis A is the vector from a random point on a sphere to its origin.
Translation
The selected adsorbate is translated by a distance of δr along an axis, A. The translation δr is drawn
from a uniform distribution between 0 and Δ , where Δ is the maximum translation amplitude. The
t t
axis A is the vector from a random point on a sphere to its origin.
Regrowth
The selected adsorbate is removed and a new adsorbate of the same species is inserted at a random
position on the substrate, with a random orientation and, if a trajectory of conformations is supplied,
with a random conformation.
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

change the current state of the system into a randomly chosen neighboring state. If the energy
decreases as a result of this step, the new state will be the starting point for the next step. If the energy
increases, on the other hand, the attempt is followed by a decision about whether to accept the
selected neighboring state or to use the current state as the starting point for the next step. This
decision is made on the basis of a random number. The probability of accepting a state of higher energy
depends on the energy difference between the states and the temperature of the system.
An essential feature of the sampling method is that it allows the system to explore states that are higher
in energy. Although this momentarily worsens the object function, the system is able to escape from
local minima and search for better ones. To steer the simulation in the right direction, the probability of
accepting a less favorable state must decrease with the value of the function to be minimized;
otherwise, the simulation would spend too much time in areas that are of no interest. The Monte Carlo
method provides just such a scenario. In this method, the probability of accepting an energy increase, E
(s') - E(s) > 0, is equal to exp{-[E(s') - E(s)]/kT}, which clearly decreases with the energy difference. The
temperature, T, multiplied by the Boltzmann constant, k, sets the scale of the energy barriers that can
be overcome.
In the simulated annealing method, the temperature is slowly decreased during the course of the
simulation. Initially, when the temperature is high, large energy increases are acceptable, allowing the
system to explore a broad region of the search space, whilst ignoring small ripples in the energy surface.
As the temperature decreases, steps that lead to an increase in energy are increasingly disfavored,
thereby steering the system to step to neighboring states with a lower energy. Eventually, when the
temperature is very low, the system is forced to evolve to the local minimum in the current region of the
search space.
At the end of an annealing simulation, the system will have reached a state corresponding to a local
minimum of the object function in an area of the search space. This state is an approximation to the
global minimum in the search space. By repeating the annealing process, it is possible to improve on the
approximation. So, starting from the local minimum reached in the previous run, the system is heated
up again and allowed to explore a broad region around this local minimum. Then, the temperature is
decreased and the system is annealed in another state of minimal energy. Repeating the temperature
cycles can give solutions that are closer to the global minimum solution.

Dialogs in Adsorption Locator
The following topic and its subtopics describe the dialogs in Adsorption Locator:
Adsorption Locator Calculation dialog
Use the Save Settings... option to save the current dialog settings.
Adsorption Locator Calculation dialog

The Adsorption Locator Calculation dialog allows you to set up and display the parameters for an
Adsorption Locator calculation.
The Adsorption Locator Calculation dialog contains the following tabs:
Setup: 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.
Energy: 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.
Location: Allows you to specify the region around the substrate in which adsorbate configurations will
be sampled.
Properties: Allows you to select the properties that will be computed as part of the Adsorption
Locator calculation.
Job Control: Allows you to specify job settings for the Adsorption Locator calculation.
Run: Runs a job using the settings specified. The results are placed in a subfolder of the current
Materials Studio project directory.
Run | Copy Script: Converts the current settings to a script and copies the script to the clipboard. Refer
to the Generating scripts topic for more information on using sections of scripts generated from a
dialog.
Help: Displays the Help topic for the current tab.
Access methods
Menu Modules | Adsorption Locator | Calculation

Toolbar | Calculation
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:

Coarse
Medium
Fine
Ultra-fine
These four levels offer progressively more accuracy at the expense of longer calculation times.
Tip: Use the Coarse quality setting for a quick assessment of the simulation, then progress to a higher
quality level to obtain more accurate results.
The Quality setting affects all relevant task parameters that control the precision of the simulation. If
any parameter is set by the user to a value different from that specified by the overall quality level, the
Quality is displayed as Customized.
Adsorbates: Specify the molecular structures of the adsorbates that are the subjects of the calculation
and their relative proportions.
Select the input documents by clicking in the Adsorbate column of the grid and selecting a 3D structure
document from the dropdown tree view of the current project.
Note: To be used for an Adsorption Locator calculation, 3D structure documents must be part of the
current project. Either create the desired molecule using the sketching tools in the Materials
Visualizer or import the required structure into the project before selecting input documents for the
simulation.
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
Menu Modules | Adsorption Locator | Calculation | Setup

Toolbar | Calculation | Setup
Simulated Annealing Options dialog

The Adsorption Locator Simulated Annealing Options dialog allows you to specify parameters that
control the simulated annealing temperature cycle and to set the relative probabilities (ratios) of the
different Monte Carlo step types.
Number of cycles: Specify the number of temperature cycles to be performed in the simulated
annealing run.
Steps per cycle: Specify the number of Monte Carlo steps between the selected limits for each
temperature cycle.
Optimize geometry: When checked, indicates that the adsorbate configurations output from the
simulation will be minimized before they are returned.
More...: Provides access to the Adsorption Geometry Optimization dialog, which allows you to specify
the algorithm to be used for the optimization phase of the simulated annealing run and to set the
associated convergence levels.
Dialogs in Adsorption Locator | Page 22

Note: The More... button is enabled only if the Optimize geometry checkbox is checked.
Automated temperature control: When checked, indicates that all the parameters controlling the
simulated annealing temperature cycle will be determined automatically by Adsorption Locator.
Maximum temperature: Specify the maximum temperature, in K, for the simulated annealing
temperature cycle. Default = 1.0e5 K.
Final temperature: Specify the final temperature, in K, for the simulated annealing temperature cycle.
Default = 100 K.
Note: The Maximum temperature and Final temperature controls are enabled only if the Automated
temperature control checkbox is unchecked.
Conformer: Specify the Ratio of the conformer step type to be used in the calculation. The conformer
step type is only used for adsorbate components for which a trajectory of conformers is supplied.
Note: The conformer step type will automatically assume a Ratio of zero for cases where no
conformers are specified for an adsorbate, that is, the input document containing the adsorbate is
not a 3D Atomistic Trajectory document.
Rotate: Specify the Ratio of the rotation step type to be used in the calculation. The rotation step type is
only used for adsorbate components with more than one atom.
Translate: Specify the Ratio of the translation step type to be used in the calculation.
Regrow: Specify the Ratio of the regrowth step type to be used in the calculation.
The values in the Probability column are automatically updated whenever any of the Ratio settings are
altered, ensuring that the total probability for all step types is always unity.
Help: Displays the Help topic in a browser.
Access methods
Menu Modules | Adsorption Locator | Calculation | Setup | More...

Toolbar | Calculation | Setup | More...
Adsorption Geometry Optimization dialog

The Adsorption Geometry Optimization dialog allows you to specify the algorithm to be used for the
optimization phase of the simulated annealing run and to set the associated convergence levels.
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.
Algorithm: Specify the algorithm to be used in the geometry optimization calculation. The following
methods are available:

Smart
Steepest descent
Conjugate gradient (Polak-Ribiere variant only)
Quasi-Newton (BFGS variant only)
ABNR (Adjusted basis set Newton-Raphson)
The steepest descent, conjugate gradient, quasi-Newton, and ABNR methods are described in more
detail in the Classical simulations theory section. The Smart algorithm is a cascade of the steepest
descent, ABNR, and quasi-Newton methods.
Quality: Set the quality of the geometry optimization calculation. The quality level determines the
convergence thresholds for energy change, maximum force, and maximum displacement between
optimization cycles. The quality level also controls which of these criteria are tested. The optimization
will stop when all of the specified thresholds are reached.
Available options are:
Coarse
Medium
Fine
Ultra-fine
Only the Energy convergence criterion is tested by default when the Quality is set to Coarse. Both
Energy and Force thresholds are employed when the Quality is set to Medium. When the Fine or Ultra-
fine settings are used, all the threshold values must be reached.
The default values of the convergence thresholds for each quality level are given in the table below:
Value Coarse Medium Fine Ultra-fine

Energy (kcal mol-1) 0.002 0.001 1 × 10-4 2 × 10-5
Force (kcal mol-1 Å-1) 2.5 0.5 0.005 0.001
Displacement (Å) 0.05 0.015 5 × 10-5 1 × 10-5
Alternatively, thresholds can be specified independently for Energy, Force, and Displacement. Select the
desired thresholds using the checkboxes and set them to the required values. If you enter your own
values for any of these thresholds, the Quality is displayed as Customized.
Energy: When checked, indicates that a convergence threshold for the specified maximum energy
change, in kcal mol-1, during the geometry optimization will be enabled.
Force: When checked, indicates that a convergence threshold for the specified maximum force, in kcal
mol-1 Å-1, during the geometry optimization will be enabled.
Stress: When checked, indicates that a convergence threshold for the specified maximum stress, in GPa,
during the geometry optimization will be enabled.
Displacement: When checked, indicates that a convergence threshold for the specified maximum
displacement, in Å, during the geometry optimization will be enabled.
Max. iterations: Specify the maximum number of geometry optimization cycles. If this number of cycles
is reached, the calculation will stop, even if the convergence criteria are not satisfied. Default = 500.
External pressure: Specify the hydrostatic pressure, in GPa, on the structure.
Note: A positive value for the External pressure indicates that the structure is under compression.

Optimize cell: When unchecked, indicates that the cell parameters will not be optimized during the
geometry optimization. This checkbox is not available for configuration.
Keep motion groups rigid: When checked, indicates that any motion groups defined for the structure
will be treated as rigid bodies during geometry optimization.
More...: Provides access to the Motion Groups dialog, which allows you to specify motion groups for
the structure.
Ignore invariant terms: When checked, invariant terms in a rigid body are ignored and will not
contribute to the energy.
Access methods
Menu Modules | Adsorption Locator | Calculation | Setup | More... | More...

Toolbar | Calculation | Setup | More... | More...
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.
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.

Charges: Select a method for calculating the atomic charges to be used in evaluating electrostatic
interactions from the dropdown list.
For the Dreiding and Universal forcefields, available options are:
Use current (default)
Charge using QEq
Charge using Gasteiger
If you choose the COMPASS, COMPASSII, cvff, or pcff forcefields, the default is Forcefield assigned, since
charge assignments are part of the parameters stored in these forcefield definitions.
More...: Provides access to further options for the selected method when either the Charge using QEq
or Charge using Gasteiger options are selected from the Charges dropdown list, opening the QEq
Options dialog or the Gasteiger Options dialog respectively.
Quality: Set the quality of the energy calculation. The quality level affects the Ewald accuracy for Ewald
and Ewald & group summations and the non-bond cutoff distance in the case of the atom-based, group-
based, and Ewald & group methods. Available options are:
Coarse
Medium
Fine
Ultra-fine
These four levels offer progressively more accuracy at the expense of longer calculation times.
Tip: This parameter can also be adjusted individually on the Adsorption Non-Bond Options dialog.
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
Menu Modules | Adsorption Locator | Calculation | Energy

Toolbar | Calculation | Energy
Adsorption Preparation Options dialog

The Adsorption Preparation Options dialog allows you to alter energy expression preparation policies so
that you can construct an energy expression that meets the requirements of the simulation.
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.

List all forcefield types: When checked, indicates that all forcefield types will be shown in the Forcefield
types list. If unchecked, only those forcefield types that are appropriate to the system in the currently
active structure document will be listed. Default = checked.
Assign: Applies the forcefield specified in the Forcefield types list to the selected atom(s) in the currently
active structure document.
Bond order
Calculate automatically: When checked, indicates that bond orders appropriate for the Universal
forcefield will be calculated automatically at the start of the simulation. These bond orders are used to
construct forcefield parameters that are used in the energy expressions. Default = checked. As with
forcefield types, bond orders can be assigned manually, though this is not recommended.
Note: Bond orders can only be calculated if the Universal forcefield is used for the simulation, that is,
the Forcefield type has been set to Universal on the Energy tab of the Adsorption Locator Calculation
dialog.
Calculate: Computes bond orders 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 bond orders calculated without affecting the original structure.
Charges
Charges: Select a method for calculating the atomic charges to be used in evaluating electrostatic
interactions from the dropdown list.
For the Dreiding and Universal forcefields, available options are:
Use current (default)
Charge using QEq
Charge using Gasteiger
If you choose the COMPASS, COMPASSII, cvff, or pcff forcefields, the default is Forcefield assigned, since
charge assignments are part of the parameters stored in these forcefield definitions.
Calculate: Determines the atomic charges on the atoms in the current selection using the specified
charge method.
Charge groups
Calculate automatically: When checked, indicates that charge groups will be calculated automatically at
the start of the simulation. Default = checked.
More...: Provides access to the Adsorption Charge Groups dialog, which allows you to calculate, define,
and remove charge groups.
Access methods
Menu Modules | Adsorption Locator | Calculation | Energy | More...

Toolbar | Calculation | Energy | More...
Adsorption Non-Bond Options dialog

The Adsorption Non-Bond Options dialog allows you to specify the settings to be used when evaluating
non-bond terms.

Select the non-bond term for which you wish to modify the summation parameters from the list at the
top of the dialog.
Summation method: Select the method to be used to determine non-bond energies from the
dropdown list. Available options are:
Atom based
Group based
Ewald
Ewald & Group - Interactions between charge groups are calculated using a group-based sum, while
all other interactions are calculated using an Ewald sum
The options available depend on the periodicity of the system and the type of interactions being
considered. For example, the Ewald and Ewald & Group options are only available when a periodic
system is in scope and Electrostatic is selected from the list view at the top of the dialog.
Truncation: Select the type of truncation of non-bond energy terms to be applied for atom-based and
group-based methods from the dropdown list. Available options are:
Cubic spline - A cubic spline of the non-bond energy terms from their full value to zero will be carried
out
None - No truncation will be applied, that is, all non-bond interactions between all atoms in the
structure will be calculated
Note: The Truncation control is enabled only if the Summation method is set to Atom based or
Group based.
A cubic spline truncation must be applied for periodic systems or if group-based summation is used.
As a result, the None option is unavailable when a periodic system is in scope or if the Summation
method is set to Group based.
Cutoff distance: Specify the cutoff distance, in Å, at which interaction energies are set to zero for atom-
based, group-based, and Ewald & group summations.
Note: The Cutoff distance control is both visible and enabled only if the Summation method is set to
Atom based or Group based and the Truncation is set to Cubic spline or if the Summation method is
set to Ewald & Group.
Ewald accuracy: Specify the accuracy, in kcal mol-1, of Ewald and Ewald & group summations.
Note: The Ewald accuracy control is visible only if the Summation method is set to Ewald or Ewald &
Group.
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.

Value Coarse Medium Fine Ultra-fine
Electrostatic/vdW Cutoff distance (Å) 9.5 12.5 15.5 18.5
Ewald accuracy (kcal mol-1) 0.01 0.001 0.0001 0.00001
If you enter your own values for either of these settings, the Quality is displayed as Customized on the
Energy and Setup tabs.
Note: The non-bond cutoff distance for hydrogen bonds is independent of the quality setting
selected for the energy calculation and so cannot be set using the Quality control on the Energy tab.
Spline width: Specify the size, in Å, of the region within which non-bond interactions are to be splined
from their full value to zero when the cubic spline truncation method is used for atom-based and group-
based summations. A spline width of zero switches off spline interpolation and is equivalent to a direct
cutoff.
Note: The Spline width control is both visible and enabled only if the Summation method is set to
Atom based or Group based and the Truncation is set to Cubic spline.
Buffer width: This control is not used in Adsorption Locator at present.
Apply long range correction: This control is not used in Adsorption Locator at present.
Use lookup table: This control is not used in Adsorption Locator at present.
Access methods
Menu Modules | Adsorption Locator | Calculation | Energy | More...

Toolbar | Calculation | Energy | More...
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
Menu Modules | Adsorption Locator | Calculation | Location

Toolbar | Calculation | Location
Bounding box selection

Checking the Bounding box checkbox on the Location tab displays a control which allows you to specify
the dimensions of the region around the substrate atoms in which adsorbate configurations will be
sampled.
Set maximum adsorption distance: When checked, indicates that the region defined by the specified
maximum distance, in Å, from the nonperiodic substrate atoms will be sampled for adsorbate inclusion.
If unchecked, Adsorption Locator will use a reasonable default value for this distance.

Note: The Set maximum adsorption distance option is enabled only if a nonperiodic system is in
scope. The bounding box for a periodic system is always the unit cell.
Access methods
Menu Modules | Adsorption Locator | Calculation | Location | Bounding box

Toolbar | Calculation | Location | Bounding box
Surface region defined by atom set selection

Checking the Surface region defined by atom set checkbox on the Location tab displays controls which
allow you to select and specify target atoms in the substrate and to specify the dimensions of the region
around these target atoms in which adsorbate configurations will be sampled.
Set maximum adsorption distance: When checked, indicates that the region defined by the specified
maximum distance, in Å, from the selected target atoms will be sampled for adsorbate inclusion. If
unchecked, Adsorption Locator will use a reasonable default value for this distance.
Add selected atoms to TargetAtoms set: Creates a set of atoms entitled TargetAtoms using the
currently selected substrate atoms in the active 3D Atomistic document. If a set named TargetAtoms has
already been defined for the active document, any of the selected atoms that are not already members
of the set will be added to it.
Note: This button is enabled only if some of the substrate atoms in the currently active 3D Atomistic
document have been selected.
Select atoms in TargetAtoms set: Selects atoms defined as a target atoms set within the currently active
3D Atomistic document containing the substrate.
Note: This button is enabled only if a set of atoms entitled TargetAtoms has been defined for the
currently active 3D Atomistic document.
Access methods
Menu Modules | Adsorption Locator | Calculation | Location | Surface region defined by atom set
Toolbar | Calculation | Location | Surface region defined by atom set
Surface region defined by field values selection

Checking the Surface region defined by field values checkbox on the Location tab displays information
about the currently selected fields in the substrate structure document.
Field selected: Displays the name of the selected fields in the currently active 3D Atomistic document
containing the substrate.
Minimum: Displays the minimum mapped field value for the selected field.
Maximum: Displays the maximum mapped field value for the selected field.
Note: The Minimum and Maximum field values are not the global minimum and maximum field
values, but are the minimum and maximum values that are rendered in the currently active 3D
Atomistic document containing the substrate.

Edit...: Provides access to the Color Maps dialog, which enables you to adjust the range of values that
are displayed for the currently selected field, among other functions.
Access methods
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
Menu Modules | Adsorption Locator | Calculation | Properties

Toolbar | Calculation | Properties
Low energy configurations selection

Checking the Low energy configurations checkbox on the Properties tab displays options for selecting
low energy configurations to be output at the end of a calculation.
Fixed number: When selected, indicates that the number of low energy configurations returned in the
output study table will not exceed the specified number. Depending on the other parameters specified
for the run, Adsorption Locator may not be able to produce the requested number of configurations
before the job ends.
Fixed energy window: When selected, indicates that all configurations whose energies are within the
specified value, in kcal mol-1, of the energy of the lowest energy structure found will be returned in the
output study table. As new 'lowest energy' configurations are found, previously accepted configurations
that fall outside the new energy range will be discarded.
Minimum energy difference: Specify the minimum difference between the energies, in kcal mol-1, of the
low energy configurations returned in the output study table. This parameter enables you to ensure
that only one representative example from each cluster of low energy structures in the configurational
space being explored by the simulation is returned.
Include original substrate and adsorbate(s) in study table: When checked, indicates that 3D structure
documents containing the initial input configurations of the substrate and the adsorbates will be
returned in the output study table.
Access methods
Menu Modules | Adsorption Locator | Calculation | Properties | Low energy configurations

Toolbar | Calculation | Properties | Low energy configurations

Energy distribution selection
Checking the Energy distribution checkbox on the Properties tab causes a graph showing the
distribution of the intermolecular energy of each adsorbate component to be generated as part of the
Adsorption Locator run.
Access methods
Menu Modules | Adsorption Locator | Calculation | Properties | Energy distribution

Toolbar | Calculation | Properties | Energy distribution
Density field selection

Checking the Density field checkbox on the Properties tab displays options for creating fields on the
substrate showing the density of each adsorbate component.
Note: Density fields can only be calculated for periodic substrates.
Grid resolution: Set the resolution level for the grid points in the output field. Available values and the
corresponding Grid interval values are:
Coarse - 0.75 Å
Medium - 0.4 Å
Fine - 0.25 Å
Ultra-fine - 0.15 Å
Grid interval: Specify, in Å, how closely the grid points in the output field should be spaced. Setting this
parameter to a value other than one of the preset values listed above will cause the Grid resolution to be
set to Customized.
Tip: A smaller grid interval (that is, finer resolution) produces a higher quality grid, but is more costly
to compute and display.
Care should be taken with larger systems as the memory requirements increase dramatically as the grid
interval decreases.
Note: Since fields are only created at the end of a calculation, no fields will be returned if a calculation
is stopped before it is complete.
Keep intermediate files: When checked, indicates that the intermediate text files used to generate the
fields will be returned in a subfolder named Intermediate within the main results folder.
Access methods
Menu Modules | Adsorption Locator | Calculation | Properties | Density field

Toolbar | Calculation | Properties | Density field
Energy field selection

Checking the Energy field checkbox on the Properties tab displays options for creating fields on the
substrate showing the intermolecular energy of each adsorbate component.
Note: Energy fields can only be calculated for periodic substrates.

Grid resolution: Set the resolution level for the grid points in the output field. Available values and the
corresponding Grid interval values are:
Coarse - 0.75 Å
Medium - 0.4 Å
Fine - 0.25 Å
Ultra-fine - 0.15 Å
Grid interval: Specify, in Å, how closely the grid points in the output field should be spaced. Setting this
parameter to a value other than one of the preset values listed above will cause the Grid resolution to be
set to Customized.
Tip: A smaller grid interval (that is, finer resolution) produces a higher quality grid, but is more costly
to compute and display.
Care should be taken with larger systems as the memory requirements increase dramatically as the grid
interval decreases.
Note: Since fields are only created at the end of a calculation, no fields will be returned if a calculation
is stopped before it is complete.
Keep intermediate files: When checked, indicates that the intermediate text files used to generate the
fields will be returned in subfolder named Intermediate within the main results folder.
Access methods
Menu Modules | Adsorption Locator | Calculation | Properties | Energy field

Toolbar | Calculation | Properties | Energy field
Job Control tab

Adsorption Locator calculations run in the background on a server through the gateway. The Job
Control tab allows you to select a server for the Adsorption Locator calculation and to control some
aspects of how the calculation will be performed.
Note: The options specified on the Job Control tab only apply to new jobs. They do not affect jobs
that are already running.
Gateway location: Select a server for the Adsorption Locator calculation from the list of available server
machines. You can add servers to the list using the Server Console.
Queue: Specify the queue to which the job will be submitted. Select the desired queue from the
dropdown list, which displays the available queues on the chosen gateway. See Working with queues for
additional details.
Job description: Specify the name to be used to identify the job.
A default job description is automatically assigned. An alternative description can be chosen by
unchecking the Automatic checkbox and entering the new name in the Job description text box.
Automatic: When checked, indicates that a job description will be selected automatically. Default =
checked.
More...: Provides access to the Adsorption Job Control Options dialog, which allows you to set
additional options associated with monitoring and controlling the results of an Adsorption Locator job.

Access methods
Menu Modules | Adsorption Locator | Calculation | Job Control

Toolbar | Calculation | Job Control
Adsorption Job Control Options dialog

The Adsorption Job Control Options dialog allows you to set the options associated with monitoring and
controlling the results of an Adsorption Locator calculation.
Update structure: When checked, indicates that intermediate results will be used to update the
displayed structure as the job progresses. Default = unchecked.
Update graphs: When checked, indicates that intermediate results will be used to update the displayed
graphs as the job progresses. Default = checked.
Update textual results: When checked, indicates that intermediate results will be used to update
textual results files as the job progresses. Default = checked.
Tip: Intermediate updates are useful shortly after initiating a job to assess if it is progressing as
expected.
Update every: Specify the time interval, in seconds, between requests for intermediate updates.
Note: The rate at which new results appear is limited by the time it takes for the Adsorption Locator
server to calculate new results. This may be significantly longer than the chosen update interval.
Retain server files: When checked, indicates that the folder on the server containing the job files will be
retained after the job is complete. Default = unchecked.
If this checkbox is left unchecked, the job files on the server will be deleted. Regardless of whether it is
checked or unchecked, copies of the results files will always be retrieved from the server, placed in the
associated project on the local machine, and displayed in the Project Explorer.
Automatically view output: When checked, indicates that the output files from the job will be opened
automatically when the calculation is complete. Files opened may include a structure document and an
Adsorption Locator output file for the main task performed by the job. Default = checked.
Notify on job completion: When checked, indicates that a dialog will be displayed when the job is
complete. Default = checked.
Tip: If you run several short jobs in one session, you may find it useful to stop the automatic display
of job completion notices and results files.
Access methods
Menu Modules | Adsorption Locator | Calculation | Job Control | More...

Toolbar | Calculation | Job Control | More...

Adsorption Locator References
Cerný, V. "A thermodynamical approach to the travelling salesman problem: an efficient simulation
algorithm", J. Optim. Theor. Appl., 45, 41-51 (1985).
Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications, 2nd
Edition, Academic Press: San Diego (2002).
Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. "Optimization by Simulated Annealing", Science, 220, no.
4598, 671-680 (1983).
Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. "Equation of State
Calculations by Fast Computing Machines", J. Chem. Phys., 21, 1087 (1953).
Adsorption Locator References | Page 36

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ADSORPTION LOCATOR GUIDE

MATERIALS STUDIO 2017

Acknowledgments and References

Page 1 | Materials Studio • Adsorption Locator Guide

Preparing the structures

Tasks in Adsorption Locator | Page 2

Page 3 | Materials Studio • Adsorption Locator Guide

Defining the adsorption region

Tasks in Adsorption Locator | Page 4

Page 5 | Materials Studio • Adsorption Locator Guide

Finding adsorption sites on a substrate

Tasks in Adsorption Locator | Page 6

Note: When using a trajectory of conformations for an adsorbate structure, it is recommended

Page 7 | Materials Studio • Adsorption Locator Guide

Setting up Adsorption Locator calculations

Tasks in Adsorption Locator | Page 8

Page 9 | Materials Studio • Adsorption Locator Guide

Setting forcefield types

Tasks in Adsorption Locator | Page 10

Page 11 | Materials Studio • Adsorption Locator Guide

Viewing output files

Tasks in Adsorption Locator | Page 12

Page 13 | Materials Studio • Adsorption Locator Guide

Using Adsorption Locator job control

Remote Adsorption Locator jobs

Adsorption Locator jobs | Page 14

Adsorption Locator file formats

File type Input or Brief description

Page 15 | Materials Studio • Adsorption Locator Guide

Generation of substrate-adsorbate configurations

Theory in Adsorption Locator | Page 16

where k is the Boltzmann constant and T is the absolute temperature.

Metropolis Monte Carlo method

Page 17 | Materials Studio • Adsorption Locator Guide

Theory in Adsorption Locator | Page 18

Page 19 | Materials Studio • Adsorption Locator Guide

Theory in Adsorption Locator | Page 20

Adsorption Locator Calculation dialog

Menu Modules | Adsorption Locator | Calculation

Page 21 | Materials Studio • Adsorption Locator Guide

Menu Modules | Adsorption Locator | Calculation | Setup

Simulated Annealing Options dialog

Dialogs in Adsorption Locator | Page 22

Menu Modules | Adsorption Locator | Calculation | Setup | More...

Adsorption Geometry Optimization dialog

Page 23 | Materials Studio • Adsorption Locator Guide

Value Coarse Medium Fine Ultra-fine

Dialogs in Adsorption Locator | Page 24

Menu Modules | Adsorption Locator | Calculation | Setup | More... | More...

Page 25 | Materials Studio • Adsorption Locator Guide

Menu Modules | Adsorption Locator | Calculation | Energy

Dialogs in Adsorption Locator | Page 26

Adsorption Preparation Options dialog

Page 27 | Materials Studio • Adsorption Locator Guide

Menu Modules | Adsorption Locator | Calculation | Energy | More...

Adsorption Non-Bond Options dialog

Dialogs in Adsorption Locator | Page 28

Page 29 | Materials Studio • Adsorption Locator Guide

Menu Modules | Adsorption Locator | Calculation | Energy | More...

Menu Modules | Adsorption Locator | Calculation | Location

Bounding box selection

Dialogs in Adsorption Locator | Page 30

Menu Modules | Adsorption Locator | Calculation | Location | Bounding box