Quantum 1 Modules

4       DMol³ Interface

This chapter contains information on how to set up and run DMol³ through the QUANTUM 1 module of the Cerius² interface.

This chapter includes:

Introduction

Additional definition of the model

Optional job control issues

Setting up and starting calculations

Analyzing DMol³ results

Tutorials

Accessing DMol³ in Cerius²

After starting Cerius², select the QUANTUM 1 card deck and then the DMOL3 card. This gives you access to functionality for setting up and running your DMol³ job and analyzing the results. The QUANTUM 1 card deck should now look something like:

Documentation

This section explains how to use the Cerius²·DMol³ interface and does not discuss the DMol³ application in any detail. To learn more about DMol³, please refer to the documentation of standalone DMol³ in DMol3--Running in Standalone, DMol3--Keyword Descriptions, and DMol3--Keyword Reference. The most recent version of this documentation can be found at MSI's website:

http://www.msi.com/doc/

DMol³ can be used to perform these basic tasks:

Single-point energy

Geometry optimization

Frequency

Transition-state search

Geometry optimization and frequency

Transition-state search and frequency

Gradient

Molecular dynamics

Simulated annealing

For all calculations, you of course first need to have a model present in Cerius². For information on building and reading in models, please see Cerius² Modeling Environment (published separately by MSI).

Phases of a typical DMol³ job

A typical DMol³ session involves several phases:

1. Setting up the job--Prepare the model and specify the calculations to be performed.

Your model may be satisfactory as built or as read in from a file, or it may be necessary or helpful to further define the model before starting the run. For example, you may want to impose constraints or find the nearest point-group symmetry (and change the model's conformation to that symmetry) before starting the run. You would use one or more of the Geometry control panels for these purposes (Additional definition of the model).

If you want to set a non-default job type (task) or choose non-default parameter values for defining the chosen task, click the Run menu item in the DMOL3 card to open the DMol3 Run control panel. The tasks are discussed in detail under Setting up and starting calculations.

2. Running and controlling the job--Once the model is set up correctly and if the default run-control parameters are satisfactory, all that is required is to click the Run menu item in the DMOL3 card to open the DMol3 Run control panel (if it is not already displayed on your screen) and then click the RUN pushbutton in that control panel.

However, you may want to define non-default job-control or file-control parameters. These topics are discussed under Optional job control issues.

3. Studying the output--Analyze the data output from the DMol³ run. After your run is complete, you can examine and graphically analyze the results. Discussion of these procedures is in Analyzing DMol³ results.

Who should read this section

If your model structure is satisfactory, you do not need to read this section and may proceed to Optional job control issues.

Read this section if you want information on:

Setting geometry constraints

Finding and setting the point-group symmetry

The DMol³ program supports partial optimizations and transition-state searches. That is, the coordinates of some atoms are allowed to vary, while the positions of other atoms remain fixed during a calculation. This can decrease computation time considerably.

The parts of the model to keep fixed or to allow to vary during optimization, molecular dynamics or simulated annealing run are specified with the DMol3 General Constraints control panel, which is accessed by selecting the Geometry/Constraints menu item on the DMOL3 card.

Defining constraints

The DMol3 General Constraints control panel contains controls that mark selected atoms as fixed or free to move for geometry optimization. If the model is molecular, this control panel allows specification of fixed Cartesian coordinates and constrained distances, angles, and dihedrals. If the model is periodic, internal coordinate constraints such as distance may be set; however, bond angle and dihedral angle constraints for periodic models are not currently supported in the Cerius²·DMol³ module. For molecular dynamics and simulated annealing, only the Cartesian coordinate constraint is supported for both molecular and periodic models.

To add a constraint, set the Constraint Type popup to the type of constraint (COORDINATE, DISTANCE, ANGLE, or DIHEDRAL) and select the atoms in the model that define the constraint. Then click the Define Constraint action button. This adds the specified constraint for this model to the list of constraints.

Editing constraints

To modify a constraint (for example, change a coordinate constraint from fixed to varying or change the distance in a distance constraint from 1.28 to 1.05 Å), select the defined constraint in the list box, then (for example) change the Constraint Type popup and/or the Distance entry box and click the Modify Constraint action button. This updates the previously defined constraint.

Displaying constraints

Click the Show Constraint action button to highlight the atoms involved in the specified constraint.

Finding and setting the point-group symmetry

With the DMol3 Symmetry control panel (which is accessed by selecting the Geometry/Symmetry menu item on the DMOL3 card), you can find the symmetry group of your model within a desired level of tolerance. You can also enforce exact symmetry upon your model and indicate to DMol³ that you want to use symmetry in the calculation.

The DMol³ program can use symmetry to classify molecular orbitals. In addition, using symmetry in certain DMol³ runs can significantly reduce the computational effort.

Finding symmetry

If you want only to find the nearest point-group symmetry group for your model but leave the model unchanged:

• Make sure that the check boxes for snapping and reorienting atoms are not checked.

• Choose a desired preset level of tolerance from the Tolerance popup or enter the tolerance value in angstroms. (If a symmetry determination fails, try decreasing or increasing the tolerance.)

• Click the Find Symmetry action button.

If you also want to enforce exact symmetry by snapping the atoms to their exact symmetry positions and/or reorienting the model to the symmetry axes, make sure that the check boxes for Snap Atoms to Exact Symmetry and/or Re-Orient Atoms to Symmetry Axes are checked when you click the Find Symmetry action button.

Reorienting the structure may significantly displace your model from its starting position. To re-center the model, click the Reset View icon (on the tool bar of the main Visualizer control panel) or press <Home> on your keyboard.

Difficult models

If you find that you need to use very large tolerance values, you should probably use the Bond Geometry control panel (accessed by selecting the Move/Bond Geometry... item from the menu bar in the main Visualizer control panel) to manually adjust the geometry before using the DMol3 Symmetry control panel.

Symmetry during the DMol³ run

For some tasks, the symmetry found in this step may optionally be included in the DMol³ run.

Optional job control issues

Who should read this section

By default, DMol³ jobs are run on the same machine on which you are running Cerius². The job is run in the background and is not automatically monitored while it runs. If this is satisfactory, you do not need to read this section and may proceed to Setting up and starting calculations.

Read this section if you want information on:

Interactive vs. background or NQS run mode

Selecting a machine and base directory

Monitoring and controlling running jobs

Transferring files from one machine to another

Interactive

In interactive mode, Cerius² displays the DMol³ output so you can monitor the progress of the jobs. However, you cannot do anything else in the Cerius² interface until the job is complete, so this is useful only for jobs that you expect to finish quickly.

You can stop an interactive job by using the Cerius² Interrupt window, which is displayed while the job is running to indicate that Cerius² is busy. If you click the INTERRUPT button and select the Stop current process ASAP option, Cerius² displays an additional dialog box from which you can confirm or cancel your request or send the job into the background.

Background

In background mode, the job runs without communicating with the Cerius² interface, and you can quit Cerius², allowing the job to run by itself. When you exit Cerius², a status file is automatically saved so that, if Cerius² is restarted, the job can be selected for monitoring or (if it has finished) the output files can be read in for analysis (see Analyzing DMol³ results).

NQS

In NQS mode, the job is submitted to the Network Queueing System, provided that this software has been installed, on the local or remote host. Once the job is queued, you can quit Cerius², allowing the job to run by itself. An NQS-mode job can be selected for monitoring or file transfer in a later Cerius² session.

Selecting a machine and base directory

Other machines

Click the Hosts arrow in the DMol3 Job Control control panel to obtain a pulldown listing machines at your site to which you can send the DMol³ job. The list contains all suitable hosts on your network (as defined in applcomm.db--for a description and example file entries, see the Cerius² Installation and Administration Guide).

Select a host by clicking its name in the list. This also closes the list. You can also close the list by clicking the triangular icon again. The host selected is displayed in the entry box. You can also enter a machine name by typing it in the entry box.

Permission and password

Depending on your site's setup, you might not have permission to run on all the machines listed in the pulldown, or you may need to specify a user ID and password to access some machines. Click the Options... pushbutton to access the DMol3 Job Control Options control panel, where you can input a User ID and Password before selecting your host machine.

Tip

Base directory

You also need to specify a working (base) directory on the host machine if the default specification is not correct. For more information on how to do this, as well as whether files need to be transferred between machines in consequence, please see the on-screen help (click the right mouse button while the cursor is over the Base Directory entry box).

Setting up NQS-mode jobs

Other controls enable you to display your NQS jobs and the supported limits on the chosen host. The More... pushbutton in the NQS Control control panel gives access to the NQS Options control panel, which allows you to change less commonly used NQS job submission flags.

Please see the on-screen help for information about all the controls in these control panels.

Monitoring and controlling running jobs

Tip

You can also monitor or kill a job that is running or import the files from a remote machine to the machine on which you are running Cerius² after your job has completed:

• Selecting a job from the Job Status list and clicking the Monitor Logfile action button opens a window showing the contents of the output file for that job. Because DMol³ jobs can run for such long periods of time, the job list is maintained between Cerius² sessions via a status file (called .MSIdmol3stat and typically located in your home directory).

• To kill a queued or currently running job, select it in the Job Status list and click the Kill Job action button.

>	xhost remote_host_name 

Transferring files from one machine to another

Note

Setting up and starting calculations

The default DMol3 Run control panel looks like:

For a given model, the most important options defining the DMol³ run are the task and the method. Several other options are used for specifying the exact nature of the calculation, e.g., the charge and spin of the system.

Starting a run

If the default options are satisfactory, you need only click the RUN pushbutton in the DMol3 Run control panel to start your run. Then proceed to Analyzing DMol³ results.

Who should read this section

Read this section if you want information on:

Handling and naming DMol³ input files

Choosing a task

Calculation methods

Atomic core representations

Specifying a basis set

Specifying charge, spin, and occupations

Calculating properties

SCF options

Molecular environment

Specifying output and run options

For additional information on the options in all the control panels mentioned in this section, please see the on-screen help.

Handling and naming DMol³ input files

To change the default root name for files associated with your run, edit the contents of the File Prefix entry box in the DMol3 Run control panel. Alternatively, you can select a root name from existing datafiles using controls on the DMol3 Input File control panel (Saving, editing, and using input files). We refer to this root (or "seed") name as run_name in this documentation.

Run title

To change the default title for your run, edit the contents of the Title entry box in the DMol3 Run control panel. This descriptive text is included in the input and output files associated with your run, to aid in file identification.

Saving, editing, and using input files

For other aspects of file handling, access the DMol3 Input File control panel by clicking the Files... pushbutton in the DMol3 Run control panel.

With the DMol3 Input File control panel, you can:

• Save your input file.

Click the Save DMol3 Input File action button to write the input file you have built up so far in your Cerius² session to disk. The filename will be run_name.input.

• Edit an existing (saved) input file.

Select a file by clicking its name in the list box, then click the Edit DMol3 Input File action button to edit this file. This automatically calls up vi (or EMACS, if it is specified by the $EDITOR environment variable) to edit the file in a separate window. If you prefer some other editor, open your editor in the usual way, then edit and save the input file. Before using this functionality, you should of course ensure that no jobs with the specified file prefix are currently running.

Cerius² allows you much flexibility in performing your studies. You could, for example, build your model and set up most of your input file via the Cerius² interface, save this file, then include extra keywords that are available in standalone but not through the Cerius² interface (please see the documentation of standalone DMol³ in DMol3--Running in Standalone, DMol3--Keyword Descriptions, and DMol3--Keyword Reference) by editing this file and saving it from the editor, and finally start your run from that edited file via the Cerius² interface (see next paragraph) or by running DMol³ in standalone mode.

• Run an existing input file.

Select a file by clicking its name in the list box, then click the Run Selected DMol3 Input File action button to start a DMol³ run from a previously saved input file. The job uses the current settings of the DMol3 Job Control panel (host machine, run mode, etc., see Optional job control issues).

• Set interface controls from an existing input file.

Select an input file by clicking its name in the list box, then click the Initialize from DMol3 Input File action button. Using an input file to set the interface controls is particularly handy if you forgot how you set any particular parameter in the interface, yet you want to have consistent settings for a series of calculations.

Only control values that do not depend on the model are set, however. This means for example, that, if the input file has constraints defined with respect to atoms in the previous calculation, the constraints are ignored and are not set for the new model. Similarly, if the first input file has different basis sets defined for element types, the basis set information is ignored.

The available tasks are:

Single-point energy

Geometry optimization

Frequency

Transition-state search

Geometry optimization and frequency

Transition-state search and frequency

Gradient

Molecular dynamics

Simulated annealing

Scan potential energy surface

A single-point energy task computes the SCF solution for the input geometry. By default, the least computationally demanding options are chosen, which sets up a calculation suitable for studying electronic structure (molecular orbitals, dipole moment, etc.).

Geometry optimization

A geometry optimization task optimizes your model to a stable geometry, that is, it locates a minimum in the potential energy surface.

If required, control over the optimization procedure is available on the DMol3 Geometry Optimization control panel, which is accessed by clicking the More... pushbutton next to the Task popup in the DMol3 Run control panel (when the Task is set to Geometry Optimization).

For information about constraining atoms during geometry optimization, please see Setting geometry constraints.

Frequency

To control aspects of how frequencies are computed, open the DMol3 Frequency control panel by clicking the More... pushbutton next to the Task popup in the DMol3 Run control panel (when the Task is set to Frequency). You can:

• Use 1-point or 2-point differencing. The finite differencing proceeds from atom to atom. On a single atom, the displacements are done in the x, the y, and the z directions. If 2-point differencing is used, then the displacements are in the order +x, -x, +y, -y, +z, -z.

• Set the length of the step size used during finite differencing.

• Decide whether to project out the 6 frequencies corresponding to translation and rotation of the model (if nonperiodic) or whether to project out the 3 frequencies corresponding to translation of a periodic model. (Note, however, that these frequencies are not necessarily zero if the model geometry was not sufficiently optimized before starting the frequency job.)

• Automatically restart an interrupted frequency calculation. The program reads the run_name.hesswk file and restarts the frequency calculation with the next finite displacement.

Control over the transition-state search (including the convergence criteria and the Hessian mode to follow) is available on the DMol3 Transition State Search control panel, which is opened by clicking the More... pushbutton next to the Task popup in the DMol3 Run control panel (when the Task is set to Transition State Search).

Tip

Geometry optimization and frequency

The geometry optimization is done with the specified input parameters, including constraints (if specified), to produce an optimized structure. Then the optimized structure is used as the starting point for a frequency calculation.

Clicking the More... pushbutton next to the Task popup in the DMol3 Run control panel (when the Task is set to Optimization & Frequency) gives you access to more controls in the DMol3 Optimization & Frequency control panel.

Transition-state search and frequency

The transition-state search is done with the specified input parameters, including constraints (if specified), to produce a transition-state structure. Then this structure is used as the starting point for a frequency calculation.

Clicking the More... pushbutton next to the Task popup in the DMol3 Run control panel (when the Task is set to TS Search & Frequency) gives you access to more controls in the DMol3 TS Search & Frequency control panel.

Tip

Gradient

Molecular dynamics

Simulated annealing

Scan potential energy surface

Calculation methods

Clicking the More... pushbutton next to the Method popup (in the DMol3 Run control panel) opens the DMol3 Method Options control panel, which gives you additional choices for controlling the calculation method.

For additional information on the options in these control panels, please see DMol3--Running in Standalone, DMol3--Keyword Descriptions, and DMol3--Keyword Reference.

Atomic core representations

NONE

ECP

AE Relativity

Specifying a basis set

Basis sets for individual atom types

For all choices, you may in addition click the associated More... pushbutton (next to the Basis Set popup in the DMol3 Run control panel) to further refine your basis set assignments, considering each element individually.

The DMol3 Basis Sets Choice control panel allows you to choose different basis sets for different elements. The right-hand list box shows all the available basis sets for the element selected in the left-hand list box. Select the one you want to use.

You can use this panel to specify the version of the basis set used. The two options available are the basis set called v4.0.0, which is recommended for COSMO calculations, and the current (default) basis set of release 3.8.

Specifying charge, spin, and occupations

Regardless of the type of calculation you want to perform, if your (non-periodic) model is not neutral you need to inform DMol³ of its charge by entering a value in the Charge entry box in the DMol3 Run control panel. Enter 0 for a neutral molecule, 1 for a singly charged cation, etc. For periodic models, the Charge must be zero.

Restricted or unrestricted spin polarization

Likewise, if you want to consider a particular spin multiplicity, click the Electronic State... pushbutton in the DMol3 Run control panel to open the DMol3 Electronic State Definition control panel. Use the Spin Polarization popup in this panel to specify a restricted or unrestricted spin calculation.

Spins on individual atoms

To set the initial spin densities on individual atoms, check the Initial Spin Populations check box in the DMol3 Electronic State Definition control panel and then click the Atomic Spin Densities... pushbutton that appears. This opens the DMol3 Starting Spin Densities control panel, which you can use to set and display the spin densities on selected atoms.

Occupations

To specify occupations, use the Selecting popup in the DMol3 Electronic State Definition control panel. Other controls appear, depending on the setting of this popup, which allow you, for example, to read in fixed occupations from a file.

Calculating properties

• You may specify all of the properties before the task calculation is launched, using controls in or accessible from the DMol3 Run control panel, in which case the properties are calculated after the specified task calculation is complete.

• Alternatively, if you discover that there are properties you want to calculate after the DMol³ run has ended, you may specify those properties by selecting the Analyze/Properties/Molecular Properties menu item from the DMOL3 card to open the DMol3 Analyze Molecular Properties control panel and submit the property calculation.

If you submit the calculation and all the appropriate restart files are available, then DMol³ just performs the properties calculation, which is usually quite brief.

However, if any restart files are unavailable, a full DMol³ run may need to be restarted, which may take a while to complete.

To specify properties while setting up the DMol³ calculation, make sure that the Calculate Electronic Properties check box in the DMol3 Run control panel is checked. If it is checked, then certain default properties such as Mulliken and Hirshfeld Analysis and HOMO and LUMO grids are calculated. You may also open either the DMol3 Molecular Properties or the DMol3 Periodic Properties control panel to specify more properties to calculate. These panels are specific to molecular or crystalline model types, respectively, and are opened by clicking the Molecular Properties... or Periodic Properties... pushbutton that appears in the DMol3 Run control panel when the Calculate Electronic Properties check box is checked. The properties specified in these panels are calculated as part of the DMol³ calculation.

Calculating properties after the main DMol³ run

If, after the DMol³ calculation is complete, you realize that you did not specify all the properties you wanted, you may specify and calculate them through the DMol³ analysis functionality:

First, load the files for analysis by selecting the Analyze/Files menu item from the DMOL3 card to open the DMol3 File Analysis control panel.

Once the files are loaded, select the Analyze/Properties/Molecular Properties or the Analyze/Properties/Solids Properties menu item from the DMOL3 card to open the DMol3 Analyze Molecular Properties or DMol3 Analyze Solids Properties control panel (depending on whether the DMol³ version chosen in the DMol3 Run control panel is Molecular DMol3 or Periodic DMol3).

These panels are similar to the DMol3 Molecular Properties and DMol3 Periodic Properties panels that are opened from the DMol3 Run control panel. However, one difference is a CALCULATE button. Clicking it starts a properties calculation without attempting to do an SCF or geometry optimization or any other type of major calculation task first.

SCF options

Molecular environment

If you want to simulate point charges, you need to save and edit the input file before running DMol³ in standalone mode or via the Cerius²·DMol³ interface using that edited file (see DMol3--Running in Standalone. DMol3--Keyword Descriptions, and Setting up sophisticated jobs through Cerius2).

The solvation effects can be included by using the COSMO model. All the tasks specified for molecular calculations can be used with the COSMO model.

Specifying output and run options

Several options for limiting the size of a DMol³ run are found on the DMol3 Run Options control panel, which is accessed by clicking the Options... pushbutton in the DMol3 Run control panel. This panel may be used to specify the number of processors to be used when you run the multiprocessor (parallel) version of DMol³.

Molecular dynamics options

The top popup on this panel allows users to choose between constant energy (constant NVE) or constant temperature (constant NVT) dynamics.

Initial velocities can be handled in two ways, controlled by the second popup.

• Random Thermal Velocities. The DMol³ application defines the initial atomic velocities according to a pseudo-Boltzmann distribution at the specified initial temperature. A random number seed can be specified if the initial atomic velocity assignment needs to be reproducible.

• Velocities from Model. Atomic velocities can be assigned to the atoms of a model with the generic Assign Velocity control panel, accessible by clicking the Assign... button. The resulting kinetic energy and temperature can be queried by clicking the Query... button.

If the Use Default Time Step parameter is checked, the time step is automatically related to the smallest mass of any particle in the system propagated by molecular dynamics or simulated annealing. Otherwise, an explicit time step can be defined.

The Atom Mass parameter controls whether the same mass is to be used for all atoms. This option is useful in simulated annealing calculations to treat the update of all atomic positions on an equal basis. The PHYSICAL setting of the Atom Mass parameter allows you to employ atomic masses defined by the Cerius² Visualizer (Use Cerius2 Atomic Masses). Otherwise, the internal defaults of the DMol³ application are employed.

Simulated annealing options

The top of the Simulated Annealing control panel deals with the initial atomic velocity assignment for molecular dynamics and simulated annealing calculations.

The middle of the Simulated Annealing control panel deals with the specification of the simulated annealing protocol. A simulated annealing protocol contains a set of stages which can be assembled in this control panel.

The bottom of the Simulated Annealing control panel defines the simulation time step and the atomic nuclear masses.

Every stage can be one of five distinct types:

1. QUENCH. The system is cooled down by varying the temperature linearly between start and final values.

2. MELT. The system is heated up by varying the temperature linearly between start and final values.

3. DAMP. Kinetic energy is removed by scaling the velocity with a given damping factor at every time step. The starting temperature and a damping factor are specified. The damping factor should be between 0 and 1.

4. NVE. Constant energy molecular dynamics.

5. NVT. Constant temperature molecular dynamics by Gauss least constraint method.

Initial atomic velocity assignment

The initial atomic velocity assignment can be done in two ways controlled by the popup at the top of the control panel:

• Random Thermal Velocities. The DMol³ application defines the initial atomic velocities according to a pseudo-Boltzmann distribution at the specified initial temperature. A random number seed can be specified if the initial atomic velocity assignment needs to be reproducible.

• Velocities from Model. Atomic velocities can be assigned to the atoms of a model with the generic Assign Velocity control panel, accessible by clicking the Assign... button. The resulting kinetic energy and temperature can be queried by clicking the Query... button.

1. Random Thermal Velocities. The algorithm is similar to what the DMol³ application employs, but will take the symmetry of the system into account and can be applied to selected atoms as well as to all atoms of a model.

2. Net Linear Velocity. A linear velocity can be assigned to a selected set of atoms, or all atoms of a model.

3. Net Angular Velocity. An angular velocity corresponding to an angular momentum with respect to a given axis can be assigned to a selected set of atoms, or all atoms of a model.

The generic velocity assignment control panel does not allow you to query the temperature that results from the combination of the three (i.e., thermal, linear and angular) contributions. This is possible in the Dmol3 Velocities control panel, opened by clicking the Query... button in the DMol3 Simulated Annealing panel, if Velocities from Model are supplied as the initial velocities. The DMol3 Velocities control panel further allows you to animate the assigned initial velocities. This functionality is accessible by clicking the Animation... button in the DMol3 Velocities control panel.

Simulated annealing protocol

The center of the DMol3 Simulated Annealing control panel sets the stages for the Simulated Annealing Protocol. The stages can be combined arbitrarily. With the exception of the NVT stage, the initial temperature of stages can be set to CONTINUE indicating that the current temperature of the simulation is used as initial temperature. For the first stage, this is only allowed if initial atomic velocities (and therefore an initial temperature) are specified.

The bottom of the DMol3 Simulated Annealing control panel defines the time step and the nuclear mass assignment.

Time step

If the Use Default Time Step parameter is checked, the time step is automatically related to the smallest mass of any particle in the system propagated by molecular dynamics or simulated annealing. Otherwise, an explicit time step can be defined.

Atomic mass

The Atom Mass parameter controls whether the same mass is to be used for all atoms. This option is useful in simulated annealing calculations to treat the update of all atomic positions on an equal basis. The PHYSICAL setting of the Atom Mass parameter allows you to employ atomic masses defined by the Cerius² Visualizer (Use Cerius2 Atomic Masses). Otherwise, the internal defaults of the DMol³ application are employed.

Scan potential energy surface options

This panel allows you to specify which internal or Cartesian coordinate will be varied as well as to specify the range of the coordinate to scan. You specify a starting and stopping value for the coordinate and the number of steps to use. At each value of the coordinate, DMol³ will perform a geometry optimization. Details of the optimization parameters are available by clicking the Optimization Controls button on the DMol3 Scan PES panel.

Defining coordinates

Use the top popup menu to select the type of coordinate you want to scan. You can select from the options:

• CARTESIAN X

• CARTESIAN Y

• CARTESIAN Z

• DISTANCE

• ANGLE

• DIHEDRAL

1. Select the atoms from the molecule while holding down the shift key and using the left mouse button. Once you have selected the appropriate number of atoms, click the Define button. The numbers of the atoms will appear in the type-in boxes, and the current value of the coordinate will appear in the Start box.

2. Type the numbers of the atoms into the type-in boxes, then press <Enter> or click the Define button. The the current value of the coordinate will appear in the Start box.

To specify the range of values to scan, use the type-in boxes labeled Start, Stop, and Steps. The coordinate will be varied systematically from the starting value to the stopping value in equally sized steps. The Start value is initialized to the current value of the coordinate; the Stop value is initialized to Start+0.2 for Cartesians or Start+10% for internal coordinates. (If Start+10% will exceed 180°, then the default will be Start-10%.) You can override the defaults by entering any real numbers for Start and Stop and any positive integer for Steps. Units are Ångstroms for distances and degrees for angles.

Displaying the constraint

Clicking the SHOW Constrained Atom button will highlight the atoms involved in the coordinate and display the value of the internal coordinate. To delete the display of the coordinate value, click SHOW a second time.

Deleting a constraint

To remove a constraint that you have defined, simply click the DELETE button.

Analysis

To understand how to analyze the results of a Scan PES calculation, refer to the section Analyzing DMol³ results.

Analyzing DMol³ results

Choosing the DMol³ output files to be analyzed

Analyzing vibrational frequencies and normal modes

Analyzing orbitals and densities

Displaying orbitals and densities as surfaces

Mapping a property onto a surface

Editing and displaying slices

Molecular dynamics and simulated annealing trajectories

Scan Potential Energy Surface results

Choosing the DMol³ output files to be analyzed

Output from the last DMol³ job completed in interactive mode during this Cerius² session is automatically selected for analysis. Any graphs produced (normal mode frequencies) are automatically displayed at the end of the run.

Otherwise, you need to specify which file you want to analyze. Do this with the DMol3 File Analysis control panel, which is accessed by selecting the Analyze/Files menu item on the DMOL3 card.

Finding your output files

The list box in the DMol3 File Analysis control panel shows the DMol³ output files (run_name.outmol) in your current directory. You can browse other directories by using the popup above the list box.

If a file named run_name.outmol corresponding to the desired job is present, the run may have ended (check for job completion with the UPDATE pushbutton in the DMol3 Job Control control panel, Monitoring and controlling running jobs). The results can be analyzed by selecting that filename from the list box.

Note

Loading the output files

By default, when you select a run_name.outmol file, the associated DMol³ model is automatically loaded into the model display window. If an infrared spectrum was produced, it is automatically displayed.

Output file identification and contents

Information about the selected output file is displayed in the Summary of Calculation list box in the DMol3 File Analysis control panel after a file is selected.

To display the complete output file in a separate window, click the Examine DMol3 output action button in the DMol3 File Analysis control panel.

DMol³ files in Cerius²

The files that are generated by DMol³ in the Cerius² interface (and required for data analysis) are:

• run_name.input--Keyword input file for the DMol³ calculation.

• run_name.car--Input coordinate structure.

• run_name.run--Run script that starts the DMol³ calculation.

• run_name.outmol--Standard output file detailing what happened during the run.

• run_name_property.grd--Output file containing volumetric property information.

• run_name.hesswk--Information about the numerical second derivatives.

• run_name.hessian--The updated Hessian file for geometry optimization.

• run_name.tpotl--Analytic representation of the Coulomb potential.

• run_name.tpvec--SCF eigenvectors and eigenvalues.

• run_name.tpsmx--Kinetic energy and overlap matrix.

• run_name.tpmesh--Information about molecular numerical integration grid.

• run_name.cosmo --Information about distribution of COSMO charges on the molecular cavity.

• run_name.arc -- Results from a Scan PES calculation: the optimized geometry at each point of the scan.

Analyzing vibrational frequencies and normal modes

Normal modes

The Display Selected Mode section of the DMol3 Vibrations control panel controls the Cerius2 model window. To animate a normal mode, select the ANIMATE tool. The Mode Scale entry box determines the maximum movement of any atom; the step number can be used to freeze the model at any step of the animation; and the total number of steps controls the smoothness and relative speed of the animation.

To simply display a normal mode (as a set of arrows superimposed on the current model), select a different arrows color if desired and check the Display with check box.

Infrared spectra

The Infrared Spectrum section of the DMol3 Vibrations control panel controls the Cerius2 graph window, which displays a plot of the infrared spectrum. The peak shape and width can be adjusted: select LORENTZIAN or DELTA to set the peak shape; enter a number in the Width entry box to adjust the Lorentzian peak width (in cm^-1).

You can also adjust the graph in the graph window using the usual Cerius² procedures to, for example, adjust the scale or view only a portion of the graph. Please see Cerius² Modeling Environment for information on viewing and managing graphs.

Scaling frequency values

Finally, you may scale the calculated frequencies by a Frequency Scale Factor so that they agree better with experimental frequencies.

Analyzing orbitals and densities

Calculating orbitals

To do this, you may specify the orbitals before starting the calculation (Calculating properties), in which case the grid files are generated as part of the original DMol³ calculation. Alternatively, after the calculation is complete, you may request that additional orbitals be generated.

Do this by selecting the Analyze/Properties/Molecular Properties menu item on the DMOL3 card to open the DMol3 Analyze Molecular Properties control panel.

Specify which orbitals are to be generated in the Orbitals section of this control panel. If the desired orbital is the HOMO or LUMO, all you need to do is check the relevant check box(es) and then click the CALCULATE pushbutton. A DMol³ properties calculation is started and calculates the specified orbitals.

If you would like to calculate an orbital other than the HOMO or LUMO, click the More... Molecular Orbitals pushbutton in the Orbitals section to open the DMol3 Additional Molecular Orbitals control panel. In this panel, specify which orbital you would like to calculate by selecting it from the list box. This panel's list box displays the available orbitals for this model, their symmetry, energy, and occupancy, and whether each is an alpha or a beta orbital.

Grid specification

You can control the resolution with which the grid is calculated, through a popup in the DMol3 Additional Molecular Orbitals control panel. LOW-resolution grids are faster to calculate and display, FINE- and X-FINE-resolution grids give higher- and highest-quality graphic output, and MEDIUM-resolution grids represent a compromise between these considerations.

Calculating densities

Types of calculations

You can calculate the total electron density, the deformation density, the density of alpha or beta spins, and/or the difference (i.e., spin density) between them. For a restricted open-shell DMol³ calculation, the alpha and beta spin densities are the same, so the beta density is not calculated.

Displaying orbitals and densities as surfaces

If you run a DMol³ job interactively, the calculated orbitals and densities are automatically displayed as surfaces as you create them. However, you would need to use the DMol3 Surfaces control panel if you want to:

• Change the transparency or color for an existing surface.

• Choose which of several calculated surfaces to display.

• Display several surfaces simultaneously.

• Display surfaces that were calculated and saved in a previous Cerius² session.

• Display a surface that was not created automatically.

Finding your surfacing files

If you want to display a currently undisplayed surface, use the Files... pushbutton to access the DMol3 Surfacing Files control panel. Select the desired run_name_property.grd file and click the LOAD button. You can use the browser popup to access directories other than the current one.

Surface specification and display

Once you have a surfacing file loaded and if the default settings in the DMol3 Surfaces control panel are satisfactory, you can click the Create New Surface action button (in the DMol3 Surfaces control panel) to create and display that surface on your model. Make sure that none of the surfaces in the list box is selected if you want to create and display a new surface in addition to those already displayed.

You can edit surfaces in several ways:

• Change the value in the Isosurface Value Range entry box to change which isovalue points within the grid are displayed when the Create New Surface action button is clicked again.

• Check or uncheck the Show Surface check box to display selected surface(s) or not.

• Click the Delete Surface action button to delete selected surface(s) from the display and the Edit Surface list.

• Change the transparency and color of surfaces with the relevant controls at the bottom of the DMol3 Surfaces control panel.

An isosurface connects points in space that have the same value of some parameter. However, you can add an additional dimension to a surface, by making a property map, which displays the values of another property as different colors on an existing displayed surface.

To do this, use the DMol3 Property Maps control panel, which is accessed by selecting the Analyze/Property Maps menu item on the DMOL3 card.

Finding your property files

Specify a property to be mapped by choosing the appropriate run_name_property.grd file from the list box and clicking the LOAD pushbutton. You can use the browser popup to access directories other than the current one.

Map specification and display

If more than one surface is displayed or has been loaded, you may need to select the one on which to map the property, using the list box in the DMol3 Surfaces control panel (Displaying orbitals and densities as surfaces).

Click the Add Property action button in the DMol3 Property Maps control panel to display the property map.

You can vary the transparency of the displayed property map with the Transparency entry box.

You can change the range and color spectrum with which to display the property map by clicking the Preferences... pushbutton to access the DMol3 Property Maps Preferences control panel.

Editing and displaying slices

Finding your surfacing files

If necessary, choose the orbital or density file to be surfaced by clicking the Files... pushbutton to access the DMol3 Surfacing Files control panel (Finding your surfacing files). Select the appropriate run_name_property.grd file from the list box and click the LOAD pushbutton. You can use the browser popup to access directories other than the current one.

Slice specification and display

Once you have loaded a .grd file and if the default settings in the DMol3 Slices control panel are satisfactory, you can click the Create New Slice action button to create and display a selected slice for your model.

However, you may want to edit the slice before displaying (or re-displaying) it.

The Edit Slice list box shows the slice(s) that are currently displayed. You can select one by clicking its name in the list box. Make sure that none of them is selected if you want to create and display a new slice in addition to those already displayed.

Check or uncheck the Show Slice check box to indicate whether to display the selected slice. Click the Delete Slice action button to delete the selected slice from the display and the list.

You can change the transparency in the Transparency entry box near the bottom of the DMol3 Slices control panel.

Positioning the slice plane

A slice is defined by its position and direction. The default position and direction are chosen so that the slice passes through the best-fit plane to the whole model or any selected atoms. A slice is created with a default position and direction and can be returned to the default position or direction by clicking the appropriate reset action button.

To change the position through which the slice plane slices the grid, use the Position arrows to move the slice up or down the perpendicular to the slice plane. The numbers show the position that the slice plane passes through. They change as you click the arrows, or you can edit them directly.

To change the direction of the line perpendicular to the slice plane (up and down which the plane can be moved), edit the numbers in the Direction entry box.

Other controls

Clicking the More Editing Options... pushbutton gives you access to the DMol3 Slice Preferences control panel, which contains additional controls that affect slices.

Plot the plane's values

To create a 2D contour graph corresponding to a selected slice plane, click the Create Slice Plot in Graph Window action button in the DMol3 Slices control panel.

Molecular dynamics and simulated annealing trajectories

The .his file contains information on the atomic coordinates, velocity, total energy, potential energy and kinetic energy of the molecular dynamics simulation at each time step, as an unformatted file. The .arc file contains information on atomic coordinates and binding energy at each time step.

Note

Scan Potential Energy Surface results

If you delete the graph, you can create a new one using the ANALYSIS card in the OFF METHODS deck. Using the Input menu item, open the file run_name.arc. You can then use the Analyze-->Statistics menu item to recreate the graph of Energy vs. geometry. To do this, go to the Analysis Statistics panel, select "Total Energy" property, and then click the Profile button.

Tutorials

Lesson 1: Computation of solvation energy, vapor pressure and partition coefficients for methanol using COSMO and COSMO-RS
Lesson 2: Exploring the CH4 + Cl -> CH3 + HCl reaction with DFT MD in DMol³
Lesson 3: Using COSMO-RS to compute thermodynamic properties of binary and ternary mixtures
In Lesson 1 COSMO and COSMO-RS are used to compute the solvation energy, vapor pressure and partition coefficients of methanol. In Lesson 2 the molecular dynamics capability of DMol³ is used to study a chemical reaction. In Lesson 3 COSMO-RS is used to compute thermodynamic properties of binary and ternary mixtures. These procedures can be used as templates and applied to more complicated systems.

Lesson 1: Computation of solvation energy, vapor pressure and partition coefficients for Methanol using COSMO and COSMO-RS

 

Go to OFF SETUP card and click on OPEN FORCE FIELD/Load. This opens up the Load Force Field pulldown. Choose the COMPASS forcefield and click LOAD. Close the Load Force Field pulldown. Go to OFF METHODS and click on MINIMIZER/Run. This opens up the Energy minimization panel. Click the Minimize the Energy button. This geometrically optimizes the methanol molecule. Once the molecular structure is optimized, close the Energy Minimization panel.

Note:  If you do not have the COMPASS forcefield, you could follow the above step by using the pcff_300_1.01 or the cvff_300_1.01 forcefield.
 

2.   Run the geometry optimization in gas phase using DMol³

Now that you have a good initial geometry from energy minimization with the COMPASS forcefield, you are ready to further refine the structure using the first principles Quantum mechanical methods of Dmol³.
 

Go to the QUANTUM1 card deck and click on DMOL3/Run to open up the DMol3 Run control panel. This is a gas phase (i.e. no solvent) run for methanol. So, choose a representative name like ch3oh_g as your File Prefix. Set the Task to Geometry Optimization.  Set the Method to Nonlocal DFT, and click the adjacent More... button to open the DMol3 Method Options control panel On the DMol3 Method Options control panel, set the Density Functional Choice to VWN-BP and the Numerical Integration Grid to FINE. Close this panel. On the DMol3 Run control panel, leave Core set to NONE, and Charge set to 0. Change Basis Set to DNP. Click More... Change the Basis Set Version to V4.0.0 and use a Real Space Cutoff of 5.50 Angstroms. Click RUN to submit a DMol3 job in the background.

Note: The above settings were chosen in anticipation of running COSMO-RS later on in this tutorial. The COSMO-RS parameters were developed using the same settings of DMol³ as described above.
 

Monitor and analyze the results.
 

Click on DMOL3/Job Control. From the list of jobs in the DMol3 Job Control panel, choose ch3oh_g and click UPDATE. This should tell you if the job is still running or is completed.  Once the job is completed you can analyze the results. Click on DMOL3/Analyze/Files. From the list of *.outmol files in the DMol3 File Analysis panel choose ch3oh_g.outmol and click SELECT. This should load the DMol3 optimized structure of methanol onto the model window, and at the same time give a brief summary of the calculation in the Summary of Calculation box. In particular note the total energy, which should be something like -115.757xxxx Hartrees.

 
 

3. Run DMol3 on Methanol in the solvent environment of water.
 

With the DMol3 optimized structure of methanol in the model window (obtained at the end of step 2 above), we are now ready to determine the change in system energy in the presence of water. On the DMol3 Run control panel, click Environment... to open the DMol3 Environment control panel. Click on COSMO Solvation. Choose WATER from the list of Solvent Used. On the DMol3 Run panel, change the Task to Single Point Energy and change the File Prefix name to ch3oh_water. Click RUN.

Note: Normally you should perform only Single Point Energy calculations with COSMO on, because in most cases the structural change from gas phase geometry is insignificant. However, for polar molecules, and in particular for Zwitterionic systems, the molecular geometry may be strongly affected by the presence of the solvent. In such situations it would be important to perform Geometry Optimization with COSMO turned on. However, the gradients in the presence of a solvent are not as precise as in the gas phase, and therefore you should use COARSE criteria when performing geometry optimization calculations in the presence of a solvent.
 

Monitor the job through the DMol3 Job Control panel. Once the run is finished, SELECT the file ch3oh_water.outmol from the DMol3 File Analysis panel. Note the total energy in the Summary of Calculation box. It should be more negative than the total energy in the gas phase, something like -115.765xxxx Hartrees. Actually, calculations with COSMO produce four different Total Energies (due to various corrections). All of these can be found toward the end of the *.outmol file. For example, in the ch3oh_water.outmol file, these are printed as: 1. Total Energy (au) [TE]      {including COSMO solvation energy, Eq. 2} =        -115.765266 2. Total Energy corrected (au) [TE(corr)]     {TE(corr) = TE + DE(corr) - DE}                 =        -115.765488 3. Total energy (au) [TE]     + Non-Electrostatic Energy                            =        -115.761168 4. Total energy corrected (au) [TE(corr)]     + Non-Electrostatic Energy                            =        -115.761390 Expression in 1 is the total energy the system SCF converges to, and appears in the Summary of Calculations box. Energy in 2 accounts for a small correction  due to the spilling of charge outside the COSMO cavity. Expressions 3 and 4 are the same as expressions 1 and 2 respectively with additional correction due to non-electrostatic solvation energy.  Use Expression 2 to study reactions in solutions, and Expression 4 for comparing energies of conformers.

 

4.   Analyze COSMO results
 

Now select the Analyze/COSMO item to open the DMol3 COSMO Surface control panel. Click the Create Surface button. Change the Resolution to FINE and click the Create Surface button again. Finally, click the Display Sigma Distribution Plot button to see the COSMO charge distribution. Click Delete Surface when you are done looking at the COSMO surface.

 

5.   Run COSMO-RS.
 

Back on the DMol3 Run control panel, click Environment... again. On the DMol3 Environment control panel, turn COSMO Solvation on again and click More..., then click on Calculate COSMO-RS Properties. On the DMol3 Run control panel, change the File Prefix to ch3oh_cosmors and click the RUN button. A message appears, suggesting that you to change the parameter settings to those have been well-validated for COSMO-RS. Click Switch Parameters Values in the warning box. This launches the DMol3 job.

Wait for the COSMO-RS job to finish.
 

6.   Analyze the results
 

In a UNIX window, open the file ch3oh_cosmors.outmol using your favorite editor.

The results should appear as follows at the end of the file:

      COSMO-RS results for compound:  ch3oh_cosmors

Temperature =     298.15  K
Delta G of hydration (in kcal/mol):       -4.60
log(vapor pressure) (in bar):             -0.61
Log K ( octanol / water ):                -0.76
Log K ( hexane / water ):                 -2.76
Log K ( benzene / water ):                -1.91
Log K ( diethylether / water ):           -1.11
 

Lesson 2: Exploring the CH4 + Cl -> CH3 + HCl reaction with DFT MD in DMol³

Select the Build/3D Sketcher... command from the Visualizer menu bar to open the Sketcher control panel. Sketch CH4 and Cl. Select the CH4 molecule and click the CLEAN button to produce a reasonable CH4 starting structure.

Now move the Cl atom to within 3 Å of one of the H atoms in CH4. (Use the control panel accessed with the Visualizer command Geometry/Measurements to measure the distance).

This hydrogen atom will be referred to as "the H atom" in the following text.

2.   Run DMol3

Go to the QUANTUM1 card deck and then to the DMOL3 card. Select the RUN item to open the DMol3 Run control panel.

Set the Task to Molecular Dynamics, the Method to Local DFT, and Basis Set to DNP.

Click Electronic State... to bring up the DMol3 Electron State Definition control panel. Set Spin Polarization to UNRESTRICTED and Occupations to THERMAL.

On the DMol3 Run control panel, uncheck the Calculate Electronic Properties option and change the seed filename under the RUN button to ch4_cl.

Click the More... button adjacent to Task to bring up the DMol3 Geometry Optimization control panel. Set the first popup to CONSTANT NVE and change Random Thermal Velocities to Velocities from Model.

Click Assign... to bring up the Assign Velocity control panel. Click the Assign Thermal Motion button to assign random velocity to all atoms in the system.

Click the Show Velocity Vectors button at the bottom of the control panel to see the velocity assignment.

Click the Set Linear and Angular Momenta to Zero button.

Select the H atom and, holding down the <Shift> key, select the Cl atom. Then click Define Direction from Selected Atoms to assign the path of reaction for C and Cl atoms.

Select the Cl atom. Enter -30 in the SPEED text box to assign a 30 Å/ps velocity in the opposite direction of the Cl atom. With the Cl atom highlighted, click the Assign Net Linear Velocity button.

Select the H atom. Enter 10 in the SPEED text box to assign 10 Å/ps velocity for the H atom. With H atom still selected, click the Assign Net Linear Velocity button for the H atom. Close the Assign Velocity control panel.

Click the More... button adjacent to Task to open the DMol3 Molecular Dynamics control panel. Set Number of MD Time Steps to 100 and Initial Temperature (K) to 2000. Close the control panel.

Go back to the DMol3 Run control panel and click the RUN button to launch the job.

3.   Analyze the result during and after job is finished

Now go to the OFF METHODS card deck and select the ANALYSIS card. Click the Input item to open the Analysis Input control panel.

Open a new model window by clicking the + button in the visualizer window. Select the ch4_cl.arc trajectory file in the control panel file browser and click SELECT. Close the Analysis Input control panel.

On the ANALYSIS card, select the Analyze/Statistics item to bring up the Analysis Statistics control panel. In the Select Properties list box, select Total Energy and click the Profile button.

Use the panel accessed by selecting the Geometry/Measurements... command in the Visualizer window to measure the C-H and H-Cl distances.

Go back to the Analysis Statistics control panel. In the Select Properties list box, select Total Energy, hold the <Crtl> key and click Distance, then click the Profile button.

A plot of distance vs. conformation appears. After you have run this for a number of time steps, you will see that the two distance-conformation curves cross each other.

Click the plot where the two lines crossed to see the corresponding structure on the model window. Click the plot (any one of the two lines) to the right of the crossing point to observe the structure on the screen. Frame #78 should be close to the transition state structure of this reaction.

On the ANALYSIS card, select the Show Frames item to open the Analysis Show Frames control panel. Click the right arrow to play the trajectory in the .arc file.

Lesson 3: Using COSMO-RS to compute thermodynamic properties of binary and ternary mixtures

• chemical potential


• activity coefficient


• partial pressure


• total pressure


• vapor phase concentration


• excess enthalpy


• excess free energy

It is strongly recommended that you perform the tutorial "Computation of solvation energy, vapor pressure, and partition coefficients for Methanol using COSMO and COSMO-RS" before this one. The former tutorial has more detailed explanations of various steps and settings involved in a COSMO/COSMO-RS calculation, and includes information necessary for such calculations with other systems.

1.   Prepare the COSMO data for ethanol and benzene
 
 

Select Build/3D Sketcher... from the Visualizer menu bar to open the Sketcher control panel. Using the control panel, sketch CH3CH2OH and clean the structure

 

Go to OFF SETUP card and click on OPEN FORCE FIELD/Load. This opens up the Load Force Field pulldown. Choose the COMPASS forcefield and click LOAD. Close the Load Force Field pulldown.  Go to OFF METHODS and click on MINIMIZER/Run. This opens up the Energy minimization panel. Click the Minimize the Energy button. This geometrically optimizes the ethanol molecule. Once the molecular structure is optimized, close the Energy Minimization panel.  Next optimize the structure in gas phase using DMol3.

 

Go to the QUANTUM1 card deck and, on the DMOL3 card, select the Run item to open the DMol3 Run control panel.  Set the File Prefix to ethanol_g.  Set the Task to Geometry Optimization.  Set the various run options to the recommended values for COSMO-RS:  Functional:      VWN-BP Basis set:      DNP Basis version:      v4.0.0 Grid resolution:      Fine Atomic cutoff:      5.5 Angstroms Click RUN to launch the calculation.  Once the calculation is finished,  bring up the geometry optimized structure on the model window. Then click on DMOL3/Analyze/Files. From the list of *.outmol files in the DMol3 File Analysis panel choose ethanol_g.outmol and click SELECT.  This should load the DMol3 optimized structure of ethanol into the model window, and at the same time give a brief summary of the calculation in the Summary of Calculation box. Note the total energy, something like -155.0961210 Hartrees, which is the gas phase SCF energy of ethanol. This number and a similar number for benzene will go into the CRS_INPUT file (discussed later) necessary for the COSMO-RS calculation.

 

Next perform a SINGLE POINT ENERGY calculation with COSMO, a pre-requisite for the COSMO-RS calculation to follow. Click Environment... to open the DMol3 Environment panel. Check the box for COSMO Solvation and set Solvent Used to CONDUCTOR.  Set the Task to Single Point Energy.  Set the File Prefix to ethanol.  Click Options... on the DMol3 Run panel to bring up the DMol3 Run Options panel, then select File Management.... On the DMol3 File Management Panel, make sure that DMol3 will save the Volumetric Properties Restart files and the COSMO results file.  Launch the calculation by clicking RUN.

 

Repeat the above steps for benzene. Use a File Prefix benzene_g for the gas phase calculation and benzene for the COSMO calculation.

After the jobs have finished, continue with the next step.

2.   Prepare the COSMO-RS input file
 
 

Create a file called CRS_INPUT in the directory that you plan to use for running the standalone DMol3 job.

 

Using your favorite text editor (e.g., vi) insert the appropriate input parameters. The recommended input for this calculation appears immediately below. An explanation of the input parameters follow at the end of this section. Note that the entries in the lines following "ethanol.cosmo" and "benzene.cosmo" correspond to the total SCF gas-phase energy

 

BINARY ethanol and benzene at two temperatures VPant       0       2       1 ethanol.cosmo -155.0961210           8.1122 1592.864 226.184 benzene.cosmo -232.3147340   6.87987 1196.76 219.161       2 2      298.15      398.15

 

Save the file CRS_INPUT in the directory that you plan to use for running the standalone DMol3 job.

 

3.   Prepare the input data for DMol³

Using your favorite text editor, edit one of the DMol3 input files that was used for the molecules in the binary mixture, say benzene.input.

 

You will need to make two changes: turn COSMO-RS on, and turn SCF Restart on. Also make sure that "Calculate" is set to "energy":  1. Add the following line (following the line "Cosmo     on"):  Cosmo_RS      on 2. Change the line "SCF_Restart    off" to:  SCF_Restart      on

 

Save the input file, in this case, benzene.input.

4.   Run the DMol³ job

Be certain you have the CRS_INPUT file, the DMol³ input file, and the saved files from the two earlier runs all in the same directory. Then run DMol³ from this directory. So, from the UNIX prompt (denoted by "%" below), type:

        % benzene.run &
 

5.   Analyze the output

The output file, benzene.outmol, contains results for a number of properties including excess enthalpy and excess free energy as a function of concentration, at each of the requested temperatures.
 
 

Open the output file, benzene.outmol with a text editor and search for the string "Thermodynamics of Binary System." Under this, you will find the computed properties for each component of the system as well as for the mixture. This is repeated for each temperature.

A portion of the output from this calculation appears below:
 
 

=============================================================                  Thermodynamics of Binary System  =============================================================    Temperature  (C):  25.00          Compound #1 :  ethanol        Compound #2 :  benzene     Vapor pressure of pure substance (in bar):    1     0.05899   Vapor pressure of pure substance (in bar):    2     0.09514    x,       molar concentration    xw,      weight concentration    mu,      chemical potential at concentration x    eint,    mean interaction energy    g,       activity coefficient    pp,      partial pressure of compound    y,       vapor phase concentration    pt,      total pressure    ex_ent,  excess enthalpy    ex_fen,  excess free energy             (energies in kcal/mol, pressure in bar)    Results for Compound #1 :  ethanol           x     xw   mu   eint    g   ln(g)   log(pp)    y  log(pt) 1.0E-08  5.9E-09 -8.066  1.426 58.235  4.064 -7.464  0.000  -1.022 1.0E-05  5.9E-06 -3.989  1.409 57.788  4.057 -4.467  0.000  -1.021 1.0E-03  5.9E-04 -1.513  0.657 38.112   3.641   -2.648 0.023 -1.012 0.010  0.006 -0.669  -0.212 15.900  2.766  -2.028  0.090 -0.983 0.020  0.012 -0.471 -0.424  11.124  2.409  -1.882  0.122  -0.970 0.050  0.030 -0.246   -0.671 6.503 1.872  -1.717  0.171  -0.951 0.100  0.061 -0.103  -0.841  4.143 1.421  -1.612  0.211 -0.937  ........   .......   .......    .......  .......  .......     .......   .......     ....... 1.000  1.000 0.417  -1.333  1.000 0.000  -1.229  1.000 -1.229         Results for Compound #2 :  benzene          x     xw     mu    eint     g   ln(g)   log(pp)    y  log(pt) 1.000 1.000  2.056  1.303 1.000  0.000 -1.022  1.000 -1.022 1.000 1.000   2.056  1.303  1.000 0.000  -1.022  1.000  -1.021 0.999  0.999   2.056 1.303 1.000  0.000  -1.022  0.977 -1.012   .....   .....    .....    .....   ..... ..... ..... ..... ..... 1.0E-08  1.7E-08  -8.096  1.425   3.454  1.240 -8.483  0.000  -1.229    Excess Enthalpy (ex_ent) and Free Energy (ex_fen)   at concentration x1, x2           x1       x2   ex_ent  ex_fen 1.0E-08 1.0E+00   0.000    0.000 1.0E-05  1.0E+00   0.000   0.000 1.0E-03 1.0E+00   0.002   -0.002 1.0E-02 9.9E-01   0.014  -0.015 2.0E-02 9.8E-01   0.022   -0.024 5.0E-02 9.5E-01   0.041  -0.047    .......   ......    ......    ...... 1.0E+00  1.0E-03   0.000  -0.004 1.0E+00 1.0E-05   0.000    0.000 1.0E+00 1.0E-08   0.000    0.000

Decide which of these properties you wish to plot. Using the text editor, cut out the data you wish to plot, and save it to a file. You can then use a number of different utilities such as xgraph on UNIX or Microsoft Excel® to plot the data.

6.   Details of the CRS_INPUT file

A sample CRS_INPUT file for the ethanol/benzene system was presented in step 2. In this section we discuss the details of the input parameters in this file. The basic form of the input is as follows. Keywords are given in the order they appear in the CRS_INPUT file. This order must be maintained whenever you create a new input file.
 
 

Keyword	Meaning
BINARY title or  TERNARY title	Use BINARY for binary mixtures, TERNARY for ternary mixtures, followed by a title if desired.
VPant  or  VPexp	This tells the program how to get the Vapor Pressure. VPant computes the pressure using the Antoine equation*. VPexp requires the user to supply the experimental vapor pressure.
Debug flag	Debug flag: 0 for normal output, 1 for extensive output
Number of compounds	use 2 for BINARY systems, 3 for TERNARY
Source for gas-phase energies	use 0 to have COSMO make an estimate of gas-phase energy  use 1 to supply your own value (typically you will supply the result of a gas-phase DMol3 calculation).
Repeat the following lines for each compound in the mixture
name	name of the file containing the COSMO data. In this example, ethanol.cosmo and benzene.cosmo
gas-phase energy	blank line if "source for gas-phase energy" is 0;  otherwise total SCF energy of the molecule.
Antoine coefficients	a,b,c coefficients of Antoine formula* if VPant;  omit completely if using VPexp (not even a blank line)
end of repeated, molecule-specific data
# temp and # compounds	# temp is the number of different temperatures;  # compounds is 2 for BINARY, 3 for TERNARY
repeat the following lines for each temperature
Temp in ºK  or  Temp followed by vapor pressure	If using VPant, supply the temperature, if using VPexp, supply temp followed by the vapor pressure of each component of the mixture
end of input file

*The Antoine equation provides an approximate formula for the log of pressure as function of temperature:

log(P) = A - B/(T+C)

where A,B, and C are empirical parameters, and C is the temperature in degrees Celsius. Several sources for these parameters are available on the world-wide web including

http://www.glue.umd.edu/~nsw/ench250/antoine.dat

http://chemengineer.miningco.com/library/weekly/aa071497.htm

To rerun the above example without using the Antoine coefficients, the input would be:
 
 

BINARY ethanol and benzene at two temperatures VPexp 0 2 1 ethanol.cosmo -155.0736739 benzene.cosmo -232.2865776 2 2 298.15 eth1 benz1 398.15 eth2 benz2

where eth1 and benz1 are the observed pressures at 298.15ºK of ethanol and benzene respectively; and eth2 and benz2 are the pressures at 398.15ºK.