NAME Read_Mopac AUTHORS Susanna Wei, Koustantinos Kakouli, Timothy G. McMullen, Yihsing Song, and Lin Hua, Saint Joseph's University, Philadelphia, Pennsylvania; and George R.Famini, U.S.Army Chemical Research, Development and Engineering Center, Aberdeen Proving Ground, Maryland. SUMMARY Name Read_Mopac Type Data Input Inputs upstream geometry Outputs geometry field 1D uniform 1-space scalar float field 1D uniform 1-space scalar float field 1D uniform 1-space scalar float string Parameters Name Type Default Min Max ---- ---- ------- --- --- Read MOPAC File string 0 0 .mno Read AMBERDATA File string 0 0 .def Write Atom Location string 0 0 .loc Coord Set integer 1 1 max_frames Energy float 0.0 float_unbound Label choice "reset" Color Atom choice "color atom by formal charge" Color Bonds choice "reset bond color" Radius Scale float 1.0 0.01 3.0 Min Charge float -1.0 -2.0 2.0 Max Charge float 2.9 0.1 2.9 Picked Atom Charge float 99999.0 float_unbound float_unbound Color Legend ON/OFF boolean 1 0 1 DESCRIPTION The Read_Mopac module reads Cartesian coordinates, bond orders and valencies, final heat of formation, and atomic charges from a MOPAC output file with mno extension. It allows users to visualize the process of a chemical reaction. Each stage of the chemical reaction is shown as a frame of the display of a molecular structure. Users can observe different stages of the chemical reaction by changing the value of the parameter "Coord Set". If the user connects the output port of the AVS Module, Animate Integer, to the parameter Coord Set then the user can see the animation of this chemical reaction. Users have the choice of coloring atoms by atom type or the formal charge value of the atom. Default bond colors are white but users can change them based on bond strength or the difference between the formal charges of the two atoms involved in that bond. Color legends of formal charge and bond strength are provided to allow the user to associate colors with their numerical values. The distribution of final heat of formation (energy) of the chemical reaction can be displayed by the Graph Viewer. Atom labels (atom names and numbers) can be displayed on the atoms in the display. Users can also choose to display only the labels of selected atoms. NOTE: 1. To show the color legend, the output port of "X output" in the Read_Mopac module must be connected to col_legend2 module. 2. The following two files are required by Read_Mopac module: (1). A MOPAC output file with mno extension. (2). A file with def extension which defines the default size and color of atoms. INPUTS upstream geometry (required). OUTPUTS Field output It contains energy values of the whole chemical reaction and is used as an input to AVS "Graph Viewer" to create an energy distribution graph of the chemical reaction. Dynamic output This output contains energy values from the first stage up to the current stage of the chemical reaction. It is used as an input to AVS "Graph Viewer" to create the Energy Distribution Graph from the first stage up to the current stage of the reaction. This allows users to see the energy value associated with the currently displayed molecular structure. X output This is used as an input to AVS Module, Col_Legend2, to define minimum and maximum values and the visibility of the color legend. Label string Input to the AVS "Label" and gives information about the color of bonds or atoms. PARAMETERS Read_Mopac File: filename of MOPAC output file with mno extension. Read_AMBERDATA File: filename of a file that defines the default size and color of atoms. Write Atom Location file: filename of a file that stores coordinates of atoms in the currently displayed molecular structure. Coord Set: current stage of the chemical reaction. Energy: energy value of the currently displayed molecular structure. Label: has the following options: ALL: displays labels of all atoms in the currently displayed molecular structure. ALL BUT H: displays labels of all atoms other than H in the currently displayed molecular structure. SELECT: displays label(s) of selected atom(s).The formal charge value of the last selected atom is the value of parameter Picked Atom Charge. RESET: erases labels of all atoms. Color Atom: has the following options: COLOR ATOM BY TYPE: colors atoms based on atom type. COLOR ATOM BY FORM CHARGE: colors atoms based on formal charge values. Color Bonds: has the following options: BOND STRENGTH: colors bonds based on bond strength. FORMAL CHARGE DIFFERENTIAL: colors bonds based on the difference between the formal charges of the two atoms involved in that bond RESET: sets bond colors to default, white. Radius Scale: Changes the size of atoms. Min Charge: defined as the minimum formal charge value of all atoms in the chemical reaction minus 0.2. Max Charge: defined as the maximum formal charge value of all atoms in the chemical reaction plus 0.2. Picked Atom Charge: the formal charge value of the last selected atom. If no atom is selected, the value of this parameter is 99999. Color Legend ON/OFF: turns the color legend on or off. EXAMPLE __________________ |animated integer| | __ | | | | | -----------|------ | | ______________________ | Read_MOPAC | |___ ___ ___ ___ _| || | | | | | | | | | -|----|--------|---|- | | | | __________|__ | | | | | || | | | | ---| | | | | label | | | | | -----| | | | | | || | | | -------- |--- | | | ___________________ | | | | |generate colormap| | | | | --------------|---- | | | | | --------- | | | ------------| --------------------|-------------- | | | | | ------ | | | | ____________|___ | | | | | | | | | | | | | | | | | --- --- --- | | | | | | | | -|-----------|- | |graph viewer | | ||_| |_|| | -------------- | | col_legend2 | | | ----------------- ---------- | | | | | |----------------- | | | | ------------------------------------ _______________|_ |geometry viewer | ----------------- RELATED MODULES geometry viewer, graph viewer, col_legend2, generate colormap, animated integer and label.