Cranium. Reader Version. User s Guide

Transcription

1 Cranium Reader Version User s Guide

2 Molecular Knowledge Systems, Inc. makes no claims or warranties with respect to the contents or accuracy of this publication, including any warranties of fitness or merchantability for a particular purpose. Information in this document is subject to change without notice. The software described in this document is furnished under a license agreement or nondisclosure agreement. The software may be used or copied only in accordance with the terms of that agreement. It is against the law to copy the software except as specifically allowed in the license agreement or nondisclosure agreement. Copyright 2010 Molecular Knowledge Systems, Inc. All rights reserved. No part of this manual may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying and recording, for any purpose without the written permission of Molecular Knowledge Systems, Inc. Cranium is a registered trademark of Molecular Knowledge Systems, Inc. Molecular Knowledge Systems and Synapse are registered trademarks of Molecular Knowledge Systems, Inc. Microsoft and Windows are registered trademarks of Microsoft Corporation. Windows is a trademark of Microsoft Corporation. September 2010 Edition ii

3 Chapter 1: Welcome Welcome to Cranium our advanced physical property estimation system. This Reader version of Cranium has all the capabilities of the complete version except for the ability to save changes. This manual introduces you to many of Cranium s capabilities including how to: Enter data for elements, chemicals and mixtures Modify and extend existing estimation techniques Draw new molecular structures for groups and chemicals Estimate the physical properties of chemicals and mixtures Control which techniques Cranium chooses for estimation Evaluate the accuracy of estimation techniques This chapter provides a quick introduction to the basic concepts of Cranium s operation and user interface. 1.1 Quick Tour This section provides a quick tour of Cranium s capabilities. Open the Sample knowledge base 1. Start the Cranium application. Cranium displays a welcome dialog. 2. Press the dialog s OK button. Cranium will then display the Open file dialog. 3. Select the Sample knowledge base (or any other knowledge base you have been provided with) and press the Open button. You can choose any of the knowledge bases that come with the Cranium application. Cranium will open and display the selected knowledge base. 1-1

4 The mkskb file extension denotes a Knowledge Base Navigation A knowledge base is a compilation of information on elements, molecular structures, chemicals, mixtures, estimation techniques and references. Values for the properties of each entity are presented on a single page of the knowledge base. These entity pages are arranged into chapters. The tabs at the top of each knowledge base window correspond to each of these chapters. Since each entity is displayed on a separate page in a chapter, navigating through Cranium primarily involves changing chapters and turning pages. Change to the Chemicals Chapter 1. Click the left mouse button on the Chemicals Chapter tab located at the top of the window. Cranium displays a page of the Chemicals Chapter. Click on a tab to change chapters 1-2

5 The navigation controls located in the toolbar enable you page through all the entities within a chapter. Move to the chapter s first page Move to the previous page Move to the chapter s last page Move to the next page View chemicals on other pages 1. Press the toolbar s right facing, hollow arrow or choose the Navigation menu s Page Forward command or press the ctrl-f accelerator keystroke. The ctrl-f keystroke is generated by holding down the control key and then press the f key. All three methods are equivalent and result in the display of the next chemical stored in the knowledge base. Navigating to the previous chemical is done by either pressing the toolbar s left facing, hollow arrow, choosing the Navigation menu s Page Back command or pressing the ctrl-b accelerator keystroke. At a chapter s first page the commands for paging backward will be disabled. Likewise, at the chapters last page the commands for paging forward will be disabled. Goto the page displaying a specific chemical 1. Choose the Navigation menu s Goto command or press ctrl-g. Cranium displays the Go To Chemical dialog. Attribute displayed for selection Only items containing this substring are shown 2. Type acetate into the Match Substring edit control. Cranium displays only those names containing this substring. Scroll through the displayed list and choose Butyl acetate. Cranium turns to the page displaying butyl acetate s properties. (If you chose to work with another knowledge base that does not contain methanol, simply choose another chemical.) 1-3

6 1.1.2 Estimating Chemical Properties One of Cranium s key capabilities is to estimate physical properties quickly, easily and accurately. To estimate a property Cranium first collects all applicable techniques, sorts them by accuracy, and then tries each one until an estimate is found. Estimate butyl acetate s physical properties 1. Choose the Compute Estimates command from the Commands menu. Cranium displays the Property Estimation Dialog. 2. Press the Estimate button. Cranium will now estimate each of butyl acetate s properties documenting its progress in the dialog. Property being estimated Once Cranium has finished estimating properties, you can examine the process by which each estimate was generated. 3. Expand the Boiling Point node and continue to expand all child nodes. The display should be similar to the following. Status of techniques available for estimating the normal boiling point This figure shows that the knowledge base has three estimation techniques that can estimate the boiling point. The first technique tried was the Antoine Equation RPP2001. This technique failed. The second technique was the Joback Method. This technique succeeded its estimate is reported at the end of the listing. The third technique was the Stein + Brown Method. This technique was not tried because an estimate had already been generated. 1-4

7 4. Click the left mouse button on the Antoine Equation RPP2001. The dialog s Details button will become active. 5. Press the Details button. Cranium displays the Detailed Estimation Results dialog. Technique being examined Typically reports the reason why a technique failed The dialog shows that the Antoine Equation RPP2001 technique failed because it did not have any parameters for butyl acetate. 6. Press the Done button to return to the Property Estimation Dialog. 7. Press the Property Estimation dialog s Save button. Cranium stores the estimates in the knowledge base and displays them on butyl acetate s page. Column of data values Column of estimated values Cranium automatically selects the best applicable estimation technique. At times you may wish to manually specify which technique Cranium should use for a particular property. Manually specify the boiling point estimation technique 1. Click the right mouse button on the boiling point field s estimate control. Cranium displays the control s command menu. 1-5

8 Right click in an estimate s edit box for the commands menu 2. Choose the Select Technique command from the menu. Cranium displays the Estimation Technique Information dialog. The property s estimation mode is currently set to Automatic Mode. In Automatic Mode Cranium selects the best applicable technique. 3. Change the Estimation Mode to Manual Mode and select the Stein + Brown Method. Choose manual mode Choose an estimation technique 4. Press the OK button. Cranium will now use the Stein + Brown Method to estimate the normal boiling point. 5. Note butyl acetate s currently estimated boiling point. Use the previous instructions to estimate butyl acetate s properties again. Note how the boiling point estimate has changed. Cranium also estimates temperature and pressure dependent properties. For such properties you must first enter temperature and pressure values. 1-6

9 Estimate methanol s vapor pressure at a series of temperatures 1. Scroll down to the data pane s Temperature Dependent section. Property control Values Type control Field s table 2. Click the left mouse button in the property control. Cranium displays the Properties dialog. This dialog lists all the temperature dependent properties current known to Cranium. Temperature dependent properties 3. Select Vapor Pressure, Liquid f(t) and press the OK button. 4. Click the left mouse button in the Values Type control. A drop down menu is displayed. Choose Estimates from the menu. You must now enter the temperatures for which you want estimates generated. 1. Click the left mouse button within the Temperature Dependent field s table. Click in the white, grid area of the table not in the column headings or row labels. Cranium displays the state variables edit dialog. 1-7

10 Temperatures for estimates 2. Double click the left mouse button in the table s first row. Cranium displays another edit dialog. Enter a value of 298 K in this dialog and press the OK button. 3. Click and hold the left mouse button in the table s second row. Cranium will highlight the row. 4. Drag the mouse downward to the fifteenth row and release the mouse button. Rows two through fifteen will now be highlighted. 5. Press the Series button. Cranium will display the Temperature Series dialog. 6. Enter 300 for the Starting temperature, change the temperature option to Temperature Increment and enter a value of 1. Count of selected rows Ending or Increment option 7. Press the OK button. Cranium will enter a series of temperatures starting at 300 K and being incremented by 1 K. 8. Press the Save button in the edit dialog. Cranium stores the entered temperatures in the knowledge base and redisplays the Temperature Dependent field s table. Temperature dependent estimates can now be generated as done previously. However, for this example you will only generate vapor pressure estimates. 1. Click the right mouse button within the Temperature Dependent field s table. Click in the white, grid area of the table not in the column headings or row labels. Cranium displays the commands menu. 1-8

11 2. Choose the Compute Estimates command from the menu. Cranium will display the property estimation dialog. 3. Press the Estimate button. Cranium will estimate the vapor pressure for each temperature value. 4. Press the Save button to have Cranium store the estimated values in the knowledge base. Vapor pressure estimates Adding New Chemicals One of the advantages of an electronic reference book over a printed one is the ease with which pages can be added and removed. Add a new chemical 1. Press the Add toolbar button (the large plus sign). Alternatively you can choose the Add Page command from the Edit menu or use the crtl-a keyboard accelerator. Add a new page to the current chapter Remove the current page from this chapter Cranium adds a new, empty chemical to the Chemicals chapter. Enter a name for our new chemical 1. Click the left mouse button in the identifier s field data control. Identifier field s data control Cranium displays the Chemical Identifier s edit dialog. 1-9

12 Enter the new chemical s name 2. Type in a name for our new chemical. You can also add a reference and comments. 3. Press the Save button. Cranium will store the values in the knowledge base and display the new name in the chemical s identifier field Editing Molecular Structure Many estimation techniques require knowledge of a chemical s molecular structure. Some techniques require only information about the chemical s family, e.g., is the chemical chlorinated. Other techniques, e.g., group contribution techniques, require a chemical s structure to be completely dissected into molecular fragments. Cranium uses a simple connectivity model to represent molecular structure. Atoms and bonds are connected into a simple graph. Enter a molecular structure for our new chemical 1. Scroll the data pane to the Chemical Structure section, located near the top of the pane, and click the left mouse button in the Structure field. Structure field s data control 1-10

13 Cranium displays the molecular structure edit dialog. Drawing canvas Drawing modes and options The tool buttons on the dialog s left is used to change drawing modes. The controls at the dialog s top are used to specify the current element and the current bond type. The large central window is the canvas on which you draw your structure. Add atoms to your molecular structure 1. Press the Atom button (the large A). Cranium now adds an atom wherever you click the mouse in the canvas pane. 2. Move the mouse onto the canvas pane and click the left mouse button several times in several different locations. Cranium creates and adds several new carbon atoms. Atom tool 3. Cranium uses the current element, specified at the dialog s top, to create new atoms at the location of your mouse click. Click the left mouse button on the elements control. Choose Oxygen from the list of available elements. 4. Click the left mouse button on the canvas pane to add a new oxygen atom. As you add each atom, Cranium adds the appropriate number of assumed hydrogens. Cranium automatically updates the number of assumed hydrogens as you bond atoms together. 1-11

14 Connect atoms by bonds 1. Press the Bond button (the diagonal line). Cranium is now ready to create bonds between atoms. 2. Click the left mouse button on the first atom to be bonded. Cranium redraws the atom in green and surrounds it with four small, solid rectangles now adds an atom wherever you click the mouse in the canvas pane. Bond tool 3. Click the left mouse button on the second atom to be bonded. Cranium creates a bond of the currently selected bond type and attaches it to this atom and the first bonding atom. 4. The current bond type is changed using the bond type control located at the top of the dialog. Click the left mouse button on the bond type control. Cranium displays a list of available bond types. 5. Choose the Double Bond type from the list. 6. Continue the process, selecting pairs of atoms to bond, until all atoms are bonded. 7. You have now completed editing your new structure. Press the Save button. Cranium will store the structure in the knowledge base and redisplay it in the structure field. You can now use the Commands menu Compute Estimates command to estimate the properties of the new structure Entering New Estimation Techniques Physical property estimation techniques are Cranium s central focus. Instead of representing estimation techniques as fixed subroutines of compiled code, Cranium considers them to be data in the same way as a mixture s composition or a material s molecular structure. Cranium thus provides you with the ability to edit existing techniques and create your own new estimation techniques. We use the example of entering a new estimation technique for the critical temperature. Although the technique is not very accurate, it is very general and vey simple to enter. The technique s model is: 1-12

15 Tc = * Tb where Tc is the critical temperature in K and Tb is the normal boiling point also in K. Enter the new estimation technique 1. Click the left mouse button on the Techniques tab located at the top of the knowledge base window. Cranium changes to the Techniques chapter. Techniques chapter 2. Add a new technique by pressing the Add button (the toolbar button with the large + sign). Cranium creates and adds the new technique page. 3. Click the left mouse button on the identifier pane s data control. Cranium displays the edit dialog. Enter a name for the technique and press the Save button. 4. The data pane s Descriptive Information section contains the Property field. This value must be entered for every technique. Click the left mouse button in the Property field s edit control. Cranium displays the Estimated Properties dialog. 5. Choose Critical Temperature from the list and press the Save button. Note that Critical Temperature and Critical Temperature f(x) are two different properties. Cranium will store the property value in the knowledge base and display the property in the field s control. Property being estimated Central to Cranium s concept of representing estimation techniques as ordinary data is the ability to enter new source code. Entered code is checked by Cranium, compiled into a small, fast set of operations, and stored within the current knowledge base. 1-13

16 Enter the new technique s estimation model 1. Scroll the data pane down to the Model Information section. The second field in this section is the Estimation Model field. Click the left mouse button in the field s data control. Cranium displays the Estimation Model edit dialog. Code editor for technique s model 2. Press the Default Args button located on the dialog s right. Cranium adds the argument declarations to the estimation code. Values for these arguments will be provided by Cranium when the estimation technique is run. 3. Enter the following code and press the Save button when finished. Cranium will check and compile the code signaling any errors it finds. // Variable declarations double tc, tb; string prop; int err; // Retrieve boiling point value prop = Boiling Point ; tb = CProp(chemical, prop, 0.0, 0.0, err); if( err!= 0 ) return FALSE; // Critical temperature estimate tc = * tb; // Set Result SetResult(tc); // Successful return TRUE; The new estimation technique can now be executed. Execute the new estimation technique 1. Change to the Chemicals chapter and go to the page displaying methanol. 1-14

17 2. Scroll the data pane down to the Critical Properties section and click the right mouse button on the Tc field s estimate control. Cranium displays the control s command menu. 3. Choose the Select Technique command from the menu. Cranium displays the Estimation Technique Information dialog. 4. Change the Estimation Mode to Manual Mode and select the Tc: New Technique method. Select our newly created technique 5. Press the OK button. Cranium will now use the New Technique method to estimate the critical temperature. 6. Click the right mouse button again in the Tc field s estimate control. From the displayed command menu select the Compute Estimate command. Cranium will display the Property Estimation dialog. 7. Press the Estimate button and then the Save button. Cranium will use the New Technique to predict the critical temperature, save the estimate in the knowledge base and display the new estimate in the field s control. Estimated by our New Technique 8. To verify that the New Technique was used to estimate the critical temperature, click the left mouse button in the Tc field s estimate control. Cranium displays the Estimation Details dialog that shows the New Technique was used. 1-15

18 9. Press the OK button to exit the dialog. Estimated by our New Technique Evaluating Estimation Techniques Our simple estimation technique seems to work very well for methanol. Will it work as well for other chemicals? Cranium provides additional capabilities for evaluation of estimation techniques. Evaluate our new estimation technique for all chemicals in the knowledge base 1. Change to the Techniques chapter and go to the page displaying our new estimation technique. 2. From the Commands menu choose the Evaluate Technique command. Cranium will display the Evaluating Estimation Technique dialog documenting each chemical as its critical temperature is estimated. When Cranium has completing compiling data and estimates it computes summary and distribution statistics and displays these results in the Technique Evaluation dialog. Our New Technique s estimation errors 1-16

19 For such a simple estimation technique its accuracy is very good Tour Summary This brief tour has demonstrated some of Cranium s core capabilities. Additional documentation can be found on our website. However, using Cranium will inevitably be the best learning experience. 1-17