How to setup calculation - Triumphany/structure GitHub Wiki
How to Optimize molecule in Gaussview
Table of content
1. Structure in the gauss view
3. Opening the Optimized structure
Overview
This page discusses setting up Gaussian calculations with GaussView. It deals only with the mechanics of doing so.
1. Structure in the gauss view
- You can create the structure in the gaussian using the tools or you can import the structure (.log, .mol,.pdb).
2. Calculation setup
-
Once the desired molecule is completed, you can use the Calculate=>Gaussian Calculation Setup menu path to open the Gaussian Calculation Setup dialog.
-
This dialog allows you to set up virtually all types of Gaussian calculations and to submit them from GaussView.
-
The route section that GaussView is generating appears at the top of the dialog, and it is constantly updated as you make selections in the dialog’s various panels.
2-1 Job Type
-
The specified type of job appears in the top popup menu.
-
The default is a single point energy calculation. The remaining fields in the panel represent common options for the selected job type.
2-2 Method
-
This panel specifies the quantum mechanical method to be used in a calculation.
-
The factory default method is a ground state, closed shell Hartree-Fock calculation using the 3-21G basis set, but you can modify this with the Gaussian Setup Preferences
The fields in the Method line specify the following items:
-
Whether the calculation is for a ground state (the default) or an excited state.
-
If the latter, then the desired excited state method should be selected.
-
If the method field is set to DFT, and the fourth field selects the B3LYP functional.
-
The wavefunction type (closed shell vs. open shell). The default is an unspecified type.
| Function | Description |
|---|---|
| Method | Quantum mechanical method to be used in a calculation |
| Basis Set | Selection of the basis set to be used in the calculation |
| Spin | The Restricted, Unrestricted, and Restricted-Open selections prepend R, U, and RO to the method keyword (respectively). |
| (*,**) | Add functions of angular momentum type 1 greater than occupied in bonding atoms. |
| Charge | The Charge fields specify the molecule’s charge. |
| Spin | The Spin fields specify the molecule’s spin multiplicity. |
Note:
1. Select the Custom item at the bottom of the basis set menu to select a basis set other than those that can be constructed via the controls in this area.
2. You may enter any basis set keyword in the name field.
2-3 Title
This panel holds a field used for the Gaussian title section (designed to contain a brief description of the job).
- Type your description into the text box.
2-4 Link0
This panel is used for entering Link 0 commands for the job.
| Information | Description |
|---|---|
| Memory Limit | Use default memory (MW) by omitting %Mem, or set explicitly |
| Shared Processor | Do not include %NProcShared in the input file. Use the value specified in the text field that appears with the option. |
| Chkpoint file | Include %Chk with a name derived from the input filename. Use the name specified in the input field. Use the ...button to navigate to a file. |
| Oldchk file | Do not include %OldChk in the input file. Include %OldChk with a name derived from the input filename. Use the name specified in the input field. |
| Read-write file | Do not include %RW in the input file. Include %RW with a name derived from the input filename. Use the name specified in the input field. |
| Linda Worker | Do not include %LindaWorkers in the input file.Use the value specified in the text field. |
Note:
1. If you remove the specification for the name and location of the checkpoint file, you will not be able to visualize output automatically from this job.
2. The Full Path checkboxes control whether an absolute path (checked) or relative path (unchecked) is placed into the %Chk or %OldChk Link 0 command.
3. However, the full path will not appear in the Edit subpanel even when the box is checked. The ... buttons allow you to select a specific file by navigating it.
2-5 General
This panel allows you to select commonly used general calculation options.
2-6 Guess
This panel contains settings related to the initial guess.
- Consult the discussion of the Guesskeyword in the Gaussian User’s Reference for full details on these options.
2-7 NBO
This panel is used to select NBO analysis at the conclusion of the Gaussian job.
2-8 Solvation
This panel allows you to specify that the calculation is to be performed in solution rather than in the gas phase. List of solvation models included in this package
- Default
- IEFPCM
- SMD
- I-PCM Model
- SCI-PCM Model
- CPCM
Choose the solvents from the list
- Water
- DMSO (Dimethyl sulfoxide)
- Nitro-methane
- Acetonitrile
- Methanol
- Ethanol
- Acetone
- Dichloro-methane (DCM)
- Dichloro-ethane
- THF (Tetrahydrofuran)
- Aniline
- Chlorobenzene
- Chloroform
- Diethyl ether
- Toluene
- Benzene
- CCl4 (Carbon tetrachloride)
- Cyclohexane
- Heptane
2-9 PCB
This panel is used to specify options to the Gaussian PBC keyword.
2-10 Additional Input Panel
The final panel in the Gaussian Calculation Setup dialog is labeled Add. Inp.
-
It may be used to enter any additional input section(s) required by the calculation you plan to run.
-
The Additional Keywords field below the panel area is used to enter any desired Gaussian keyword and/or option.
Note
1. You must include the keyword for every option in this field even if it already appears in the route section as a result of panel item selection.
2-11 Preview
In the review window check the input file.
-
This review file includes all the details of the numbers of atoms and their coordination.
-
All the details of the calculation methods, basis sets, spins, etc. must be shown in the preview.
2-12 Submit
The buttons at the bottom of the dialog have the following effects:
- Submit: Starts a Gaussian calculation using the current input file. You will be prompted to save the input file if you have not already done so.
- Quick Launch: Launches a Gaussian job without further ado (more information here).
- Cancel: Closes the dialog box and returns all selections to their default values.
- Edit: Allows direct access to the input file with an external text editor. The input file is not available for editing until it has been saved with Gauss View.
- Retain: Closes the dialog box. Current selections are retained, but the input file is not created/updated, and no Gaussian job is submitted.
- Defaults: Returns all items to their default values.
3. Opening the Optimized structure
Locate the output (.chk file) from the system that you have set in the link O. Click on File=> Open, then select the .chk file and open the file.