Advanced Visualization for Chemistry

(1)

Advanced Visualization

for Chemistry

Part 11

–

Tools customization

Mario Valle

March 7

–

8, 2006

Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006

Why we need customization

Read new file formats

Compute and fuse together new derived quantities

Add (computed) new graphical elements in the view

Integrate visualization with some computational code

Visualization is almost ok, but…

What the tools offer

Save “status”

Scripting language interface

TCL

Python

V (for AVS/Express)

C++ API

(2)

STM3 customization

1. Save application network

2. Modify or create V macros

3. Create modules

AVS/Express architecture

Object Manager

AVS/Express project structure

avsenv

templ.v

v/

express.exe

pc/

bin/

lib/

include/

module1/

bld/

express.*

xexpress.*

user.*

xuser.*

prj

Save Project - Workspace content

XP_PATH

(3)

Create a user interface

Add Module Wizard (1 of 3)

(4)

Interface between V and code

AVS/Express

Code

Module

definition

Interface

Code

Parameters

Behavior

Generated by the wizard

Extensibility

–

MolecularDataType

group MolecularDataType {

int

num_atoms;

// total number of atoms

int

atom_z[.num_atoms];

// atomic numbers list

string atom_name[.num_atoms];

// atom names as read from the file

string residue_name[.num_atoms];

// residue names

int

residue_id[.num_atoms];

// residue number

float

xyz_lst[.num_atoms][3];

// atom coordinates

float

charge_lst[.num_atoms];

// atom charge or generic parameter

int

num_bonds;

// numeber of bonds

int

connect_lst[2*.num_bonds];

// connection list

int

bond_type_lst[.num_bonds];

// type of bond; the values are defined in mol_type.h

float

offset_lst[.num_atoms][3];

// atom offsets provided by some formats

group unit_cell {

// info on unit cell placement

float

side_vectors[3][3];

// vectors defining the three unit cell sides

float

angles[3];

// angles between unit cell sides

float

origin[3];

// the origin of the unit cell

};

group symmetry {

// info on atom symmetries

string

space_group;

// the space group symmetry group label

};

(5)

VMD customization

Source a TCL script

Package a script as an extension

Add your code as a loadable TCL command

Adding a new format reader

TCL

To execute Tcl commands, you will be using a

convenient text console called Tk Console.

Select the Extensions

Tk Console menu item.

VMD TCL commands

Sleep a number of seconds before reading another command. Animation is frozen. sleep

Wait a number of seconds before reading another command. Animation continues. wait

(Tcl) Get information about this version of VMD vmdinfo

Add new keyboard commands. user

Translate the objects in the current scene. translate

Initialize and control external spatial tracking devices. tool

Position a checkerboard stage on the screen. stage

Scale the current scene up or down. scale

Rotate the current scene around a given axis by a certain angle. rotate

Rotate the current scene continually at a specified rate. rock

Output the currently displayed image (scene) to a file. render

Start executing text commands from a specified file. play

Change the current state (mode) of the mouse. mouse

Get information about a molecule or loaded file. molinfo

Load, modify, or delete a molecule. molecule or mol

Control or query the on-screen GUI menu forms. menu

Measure properties of moleculear structures. measure

Create new material definitions and modify their settings. material

Turn on/off logging a VMD session to a file or the console. logfile

Control the light sources used to illuminate graphical objects. light

Turn on/off labels for atoms, bonds, angles, dihedral angles, or springs. label

Control the connection to a remote simulation. imd

Display an on-line help file with an HTML viewer. help

Quit VMD. exit, quit

Change various aspects of the graphical display window. display

(Tcl) Obtain color properties for various objects colorinfo

Change the color assigned to molecules, or edit the colormap. color

Position a set of XYZ axes on the screen. axes

Create atom selection objects for analysis. atomselect

Play/Pause/Rewind a molecular trajectory. animate

(6)

The Draw command

point {x y z}

line {x1 y1 z1} {x2 y2 z2} [width w] [style solid|dashed]

cylinder {x1 y1 z1} {x2 y2 z2} [radius r] [resolution n] [filled yes|no]

cone {basex basey basez} {tipz tipy tipz} [radius r] [resolution n]

triangle {x1 y1 z1} {x2 y2 z2} {x3 y3 z3}

trinorm {x1 y1 z1} {x2 y2 z2} {x3 y3 z3}

{nx1 ny1 nz1} {nx2 ny2 nz2} {nx3 ny3 nz3}

sphere {x y z} [radius r] [resolution n]

text {x y z} “text string” [size s]

Example: MultiMSMS plugin

Problem: if you have a

trajectory and want to use

the MSMS representation,

the surface is recomputed

for each timestep.

Why do not compute them

once and simply redisplay

them when needed?

So I developed the

MultiMSMS plugin using

pure TCL/Tk

<http://www.cscs.ch/~mvalle/ChemViz/multimsms.html>

Add computational code

SWIG wraps C and C++ code

as a scripting language

loadable extension

(7)

Something to take home

1. Some tools could be extended

2. The “What” is more important than the “How”

3. Ask! We are eager to extend our tools

Next steps

OK, visualization is not only presentation, but

communication is really important for a scientist

Advanced Visualization

for Chemistry

Thanks for your attention!

Mario Valle

http://www.cscs.ch/~mvalle/

[email protected]