1. No category

12/12/2012
Tutorial plan
STM4 components
and structure
Mario Valle
USPEX workshop – Stony Brook – 10/12/2012
How to analyze thousands of complex crystal structures in a minute
Logistic information
 Login on the tutorial machines with:
CrystalFp
batch
AVS/Express
concepts
CrystalFp
STM4
components
Other
STM4
modules
STM4
crystallographic
support
Ready? Go!
STM4 components
and structure
 Username/Password: look on the screen saver
 Test data files are under:
 CSCSlib/stm4-examples/data
 Run STM4 with:
CrystalFp
batch
AVS/Express
concepts
CrystalFp
STM4
components
Other
STM4
modules
STM4
crystallographic
support
 Start button  Crystallography Conference Software
 STM4  go
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
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12/12/2012
Start STM4 (and 2″ tutorial)
STM4 is a framework
for the development of
unusual and enhanced techniques
for chemistry visualization
 Launch AVS/Express (with STM4 included):
$ express
(Linux)
C:\> cd CSCSlib
C:\CSCSlib> go.bat (Windows)
 Go to Libraries  STM4
 Then go to the rightmost column (Full Apps)
 Drag the MolDisplayApp block in the gray area below marked
Applications
 In the window that pops up select the file format (e.g. PDB)
and read a file.
(few examples in: CSCSlib/stm4-examples/data)
 Mouse rotate. Middle Mouse Button+Shift: Zoom. +Ctrl: Pan.
Reset with the
button.
 With the Modules drop down menu (top left) select Display
Structure and change the molecule appearance to CPK.
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
STM4 functional areas
Access to the STM4 library
Libraries
Viewer control
Modules
GUI
View results
Build area
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STM4 modules (look at them)
A
B
C
A.
B.
C.
D.
E.
F.
G.
H.
I.
J.
K.
D
E
F
G
H
I
J
The prebuild CrystalDisplayApp
K
Readers and writers: chemical formats, screenshots and movies
Bonds related modules: compute, count and edit
Modules that compute various derived structures
Atoms selection by various criteria
Trajectory related modules
Crystallography support modules: symmetries, replications, etc.
Visualization of volumetric data like Gaussian cubes
Structure display and related graphical objects
Probe, interaction and measurements
Ready to run applications (plus display of the STM4 version)
Specialized modules (like USPEX output analysis applications)
The other components
STM4 applications
 An application is composed by modules connected together
 Colors of connection ports and lines are related to data type (only compatible types can connect)
 Each module starts when it receives all the needed data
 The user interface docks in the right place automatically STM4 pre built application CrystalDisplayApp
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
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12/12/2012
Another application example
STM4 data types
Molecule Data Type
Standard AVS Field
Display
Parameters
Geometries
Screen Image
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
STM4 module documentation
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
STM4 resources
 STM4 main pages
http://mariovalle.name/STM4/
 The STM4 modules documentation
http://mariovalle.name/STM4/doc/STM4/
 STM4 download
http://mariovalle.name/STM4/download.html
 The original STM3 paper (please cite it if you use STM4)
M. Valle, STM3: a chemistry visualization platform,
Zeitschrift für Kristallographie, vol. 220, no. 5-6, pp. 585-588, 2005
 A user level AVS/Express course
http://mariovalle.name/AVS/introduction-to-xp.html
 A (marketing) brochure on AVS/Express
http://www.avs.com/software/soft_t/avsxps.html
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
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12/12/2012
New topic
STM4 architecture has…
STM4 components
and structure
CrystalFp
batch
AVS/Express
concepts
CrystalFp
STM4
components
Other
STM4
modules
STM4
crystallographic
support
…AVS/Express behind the scenes
What is AVS/Express?
A multiplatform development environment…
…for 3D visualization applications
…object oriented
…based on a visual programming paradigm
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
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12/12/2012
Viz techniques
More than 500 visualization
techniques available
Readers available for a broad
range of file formats
Network Editor: the build area
Applications are
built dragging
modules from the
libraries to the
Network Editor
Network Editor
AVS/Express prototyping
support helps to find the
most useful technique
Any technique can be
adapted to suit specific user
requirements
Dataflow architecture
Dataflow architecture
Wait
Wait
Wait
Wait
Wait
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
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12/12/2012
Dataflow architecture
Dataflow architecture
Enter filename
Wait
Wait
Valid data
Wait
Execute
Wait
Wait
Wait
Wait
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
Dataflow architecture
Dataflow architecture
Enter filename
Wait
Valid data
Not valid
data
Wait
Wait
Wait
Wait
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
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12/12/2012
Dataflow architecture
Valid data
Dataflow architecture
Valid data
Execute
Wait
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
The result of this application
Execute
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
Data Viewer
Editors (access to rendering parameters)
Quick access
Viewer
Module GUI
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
Status panel
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12/12/2012
Not only visualization: UI Kit
AVS/Express modules with STM4
One of the advantage of STM4 is the possibility
to mix AVS/Express standard modules with
STM4 ones
AVS/Express modules in STM4
Save your work
Use extension .v
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12/12/2012
Various AVS/Express editions
 AVS homepage: http://www.avs.com/
 Developer Edition
 Official documentation: http://help.avs.com/Express/
 Everything you need
 Modules to develop applications
 Standard modules can be opened
 AVS forum: http://forum.avs.com/
 AVS/Express built‐in examples
 Visualization techniques book (in the AVS/Express manuals)
 Visualization Edition




Some AVS/Express resources
 International AVS Center (IAC): http://www.iavsc.org/
Some modules not available
Cannot create runtimes
Cost less
No differences if you are
an End User
 IAC training material: http://www.iavsc.org/training
 Patches, doc and examples: ftp://ftp.avs.com/pub/express/
 Other resources on: http://mariovalle.name/AVS/
STM4 works with both editions
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
New topic
 A user level AVS/Express course:
http://mariovalle.name/AVS/introduction‐to‐xp.html
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
Getting Started with CrystalFp
STM4 components
and structure
CrystalFp
batch
AVS/Express
concepts
CrystalFp
STM4
components
Other
STM4
modules
STM4
crystallographic
support
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12/12/2012
CrystalFp applications
Load the structure file
CrystalFp no energy
CrystalFp with energy
CrystalFp with energy
and energy landscape
Secret fantastic new
CrystalFp version
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
Load the energy file
Initialize CrystalFp, load data
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Compute fingerprints & distances
Adjust grouping (if needed)
Analyze results
Build scatterplot
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12/12/2012
Scatterplot diagnostics
Build energy landscape
Structure alignment
New topic
STM4 components
and structure
CrystalFp
batch
AVS/Express
concepts
CrystalFp
STM4
components
Other
STM4
modules
STM4
crystallographic
support
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12/12/2012
Start with CrystalDisplayApp
Add tetrahedra
Add title, logo and background
Measure a structure
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Output Image (screenshot)
Crystallography support
Create Movie
Crop Structure
 Replicate Lattice Replicate the structure unit cell along the three base
vectors.
 Apply Symmetries Compute new atoms positions from the space group
of the input molecule.
 Shift Unit Cell Shift the unit cell to re-center periodic phenomena that are
split between the opposite sides of the cell.
 Enlarge Unit Cell Add atoms outside the unit cell by different criteria.
 Move Structure Translate and rotate a given structure modifying all
atoms coordinates.
 Crop Structure Inside a geometric shape (cube, sphere, tube,…)
 Crop From Plane Remove atoms that are located more than a given
value from a plane.
 Miller Plane Crop atoms using the plane identified by given Miller indices.
 Draw Polyhedra Draw polyhedra around selected atoms
 Draw Simple Polyhedra Draw polyhedra around atoms selected by
distance only
 X Ray Structure Factor Compute and display simplified X-Ray structure
factors.
 Remove Border Atoms Remove atoms connected to atoms outside the
unit cell.
 Merge Unit Cell Apply the unit cell of one structure to another one.
 Find Symmetries Using KPLOT program.
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12/12/2012
Find symmetries
Fermi surfaces (reads EIGENVAL)
Find enthalpy transitions
Convex-hull method support
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12/12/2012
New topic
STM4 modules
STM4 components
and structure
CrystalFp
batch
AVS/Express
concepts
CrystalFp
STM4
components
Other
STM4
modules
STM4
crystallographic
support
Pre-built applications
A
B
C
A.
B.
C.
D.
E.
F.
G.
H.
I.
J.
K.
D
E
F
G
H
I
J
K
Readers and writers: chemical formats, screenshots and movies
Bonds related modules: compute, count and edit
Modules that compute various derived structures
Atoms selection by various criteria
Trajectory related modules
Crystallography support modules: symmetries, replications, etc.
Visualization of volumetric data like Gaussian cubes
Structure display and related graphical objects
Probe, interaction and measurements
Ready to run applications (plus display of the STM4 version)
Specialized modules (like USPEX output analysis applications)
MolDisplayApp
 Ready to run applications
 MolDisplayApp Read and display a molecule.
 CrystalDisplayApp Read and display structures
with symmetries and unit cell replication.
 VolumeDisplayApp Structure plus volumetric data
 PickDisplayApp Measure structure
 TracesDisplayApp Trace the motion of atoms
 PickUnitCellApp Redefine the molecule unit cell
by corner picking and crops the structure inside
the new unit cell.
 FermiSurfacesApp and FermiBandsApp Display
data from the EIGENFILE
 MultiComponentApp to support the convex-hull
method
 Plus the STM version string
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Readers/writers
STM4 – formats supported
 Readers and writer for various, static and
dynamic, chemical file formats plus movies and
images production.
 Read Structure Read a structure from file (Read
Structure No Bonds idem without computing bonds).
 Read Scalar and Read Vector Read a set of scalar
or 3D vector values from a file.
 Make Movie Capture a sequence of frames, one for
each different viewer content, and assemble them in
a movie (AVI or MPEG).
 Output Image Save a snapshot of the content of the
current viewer.
 Write Structure Write a structure to a file
 Write POV Ray Write the graphical scene for raytracing
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
Two static structures
Display
 Rendering of chemical structures and other graphical objects.
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Draw Structure and Draw Sw Structure Render structures
Info Sets Editor Edit render characteristics
Display Unit Cell Displays the borders of the unit cell.
Set Rendering Mode To change the rendering of only some atoms
Axis Glyph Display three arrows to mark the origin and the XYZ axis
directions, or the unit cell abc vectors. The glyph could also be offset
from the origin.
Background Fade Provide a colored backdrop for which you can set
the four corners colors.
Logo Create a logo image to be added to a viewer.
Enclosing Ellipsoid Compute an ellipsoid that encloses the given set
of atoms.
Time Legend Display a progress bar to show the current timestep or
current time for an animated molecule trajectory.
Color Legend Display a legend for the structure representation
colors.
Discrete Legend Color swatches for discrete data (eg. bond count)
Smooth Tube Create a tube that connect all the given points.
Error Tube Create a tube with a radius proportional to the values
associated to the connected points.
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Display structure
Bonds
 Bonds computation, editing and management.
 Compute Bonds Compute atomic bonds.
 Count Bonds Add as atom data the atom's number
of bonds.
 Count H Bonds Count the number of H Bonds
present in the input structure. The count is added
to the structure global data.
 Compute Selected Bonds Add bonds for each
atom individually plus coordination tetrahedra
 Set Manual Bonds Manually add bonds between
atoms.
Compute Selected Bonds
Compute derived structures
 Modules that compute derived structures.
 Solvent Excluded Surface Compute the molecule
Solvent Excluded Surface.
 Backbone Compute a protein backbone.
 General Backbone Display a tube through user
selected atoms.
 Vector Glyph Display with arrows the vector data
associated with a given structure.
 Merge Values Add a new scalar or vector data to
atoms, bonds or globally to the given structure.
 Atoms Values Trasp Render atoms with transparency
dependent on the associated scalar value
 Particle Density Compute the average particle mass
density using uniform binning.
 Interpolating Plane Build the least square plane
interpolating a set of picked atoms (n ≥ 3).
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Interactivity (probe & measure)
Measure a structure
 Interact with the structures: measure and
editing.
 Measure Structure Access information about and
measure a displayed structure.
 Measure Closer Atoms Measure intra-atomic
distances between a given atom and the
surrounding ones in a given range.
 Pick Unit Cell Redefines the unit cell for the
displayed structure by picking on four atoms.
Measure closer atoms
Select subsets
 Selector modules to extract a subset of
the atoms.
 Select Atoms Select specific atoms.
 Select Fragments Select specific structure
fragments (i.e. residues).
 Threshold Data Select atoms whose
associated scalar value meets various
criteria.
 Delete Atoms Interactively delete atoms.
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12/12/2012
Data threshold
Trajectories
 Modules related to dynamic data.
 Accumulate Traces Accumulate traces
(accumulated positions) for specific atoms
in a sequence of time steps.
 Accumulate Global Data Accumulate a
global scalar data in a form suitable for
charting.
 Interpolate Sequence Linearly interpolate
a given number of positions between each
pair of timesteps.
 Velocity Mean Compute the average
particle velocity using uniform binning.
Accumulate atoms traces
Volumetric data support
 Rendering of volumetric data like Gaussian cubes.
 Isosurface Create an isosurface for a given scalar value.
 Orthoslice Create an orthoslice for a given scalar value.
 Volume Render Volumetric render of a scalar valued
volume.
 Cube on Surface Assign to a surface the values of the
volume in which the surface is immersed in the positions
occupied by the surface itself.
 Cut Surface Cut a surface (eg. a Solvent Excluded Surface)
with a plane.
 Bicolor Surface Color a surface on one side with a user
specified color leaving the other one with its original
coloring.
 Interpolate Volume Interpolate a given scalar volume
adding points between original grid points.
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Access volumetric data
Volume rendering
New topic
Scripts differences
STM4 components
and structure
CrystalFp
batch
AVS/Express
concepts
On Windows
CrystalFp
STM4
components
Release\cfp.exe ^
‐‐verbose=1 ^
‐‐elements=“Si O” ^
SiO2‐24atoms.poscar ^
SiO2‐24atoms.enthalpies
On Linux
./cfp \
‐‐verbose=1 \
‐‐elements=“Si O” \
SiO2‐24atoms.poscar \
SiO2‐24atoms.enthalpies
Script.bat
Other
STM4
modules
Script.sh
STM4
crystallographic
support
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
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12/12/2012
Usage:
CrystalFp [options] POSCARfile [ENERGIESfile]
‐v ‐‐verbose (optional argument)
Verbose level (if no argument, defaults to 1)
‐? ‐h ‐‐help (no argument)
This help
‐t ‐‐elements (required argument)
List of chemical elements
‐es
‐‐max‐step ‐‐end‐step (required argument)
Last step to load (default: all)
‐ss
‐‐start‐step (required argument)
First step to load (default: first)
‐et ‐‐energy‐per‐structure (no argument)
Energy from file is per structure, not per atom
‐e ‐‐energy‐threshold (required argument)
Energy threshold
‐r ‐‐threshold‐from‐min (required argument)
Threshold from minimum energy
‐c ‐‐cutoff‐distance (required argument)
Fingerprint forced cutoff distance
‐n ‐‐nano‐clusters ‐‐nanoclusters (no argument)
The structures are nanoclusters, not crystals
‐b ‐‐bin‐size (required argument)
Bin size for the pseudo‐diffraction methods
Generate data
./cfp \
‐‐verbose=3 \
‐‐elements="Si O" \
‐‐end‐step=50 \
‐‐cutoff‐distance=30 \
‐‐fingerprint‐method=0 \
‐‐distance‐method=0 \
‐‐grouping‐method=1 \
‐‐grouping‐threshold=0.05 \
‐‐remove‐dupl=map.dat \
‐‐checkpoint‐dir=./chk \
‐‐summary=summary.dat \
‐‐fld‐fingerprints=fp.fld \
‐‐fld‐distances=dist.fld \
‐‐sorted‐distances=sorted.dat \
‐‐analysis=25 \
‐‐analysis‐file=analysis.csv \
SiO2‐24atoms.poscar SiO2‐24atoms.enthalpies
‐p ‐‐peak‐size (required argument)
Peak smearing size
...
Visualize results using R
source('readers.r')
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
It does also scatterplots!
./cfp \
source('readers.r')
# Read sorted distances and display on a log‐log chart
‐‐end‐step=50 \
# Prepare the color palette
s <‐ readSortedDist('sorted.dat')
‐‐verbose=3 \
n <‐ 256
plot(s, type='l', log='xy', xlab='Distance', ylab='Cumulative frequency',
main=bquote(paste(SiO[2], " 24 atoms")))
‐‐elements="Si O" \
pal <‐ heat.colors(n)
‐‐fingerprint‐method=0 \
‐‐distance‐method=0 \
# Display distances
d <‐ readDists('dist.dat')
image(1:ncol(d), 1:nrow(d), d, col=rev(heat.colors(15)), xlab='Fingerprint1', ylab='Fingerprint2', main=bquote(paste(SiO[2], " 24 atoms")))
# Display all fingerprints and one specific fingerprint (n. 25) with reference lines
‐‐grouping‐method=1 \
‐‐grouping‐threshold=0.05 \
‐‐remove‐dupl=map.dat \
‐‐scatterplot \
# Output the scatterplot
x <‐ readScatterplot('scatterplot.dat')
idx <‐ cut(x$value, seq(min(x$value), max(x$value),
length.out=n+1), labels=FALSE, include.lowest=TRUE)
plot(x$x, x$y, xlim=c(‐1,1), ylim=c(‐1,1), col=pal[idx],
pch=16, cex=1)
‐‐scatterplot‐file=scatterplot.dat \
# Output the corresponding diagnostic chart
f <‐ readFp('fp.dat')
‐‐diagnostic‐file=diagnostic.dat \
x <‐ readScatterplot('diagnostic.dat')
image(1:nrow(f), 1:ncol(f), f, col=rev(heat.colors(15)), xlab='Fingerprint', ylab='Distance',
main=bquote(paste(SiO[2], " 24 atoms")))
‐‐scatterplot‐param iterations 200 \
plot(f[25,], type='s', xlab='Distance', ylab='Fingerprint value',
main=bquote(paste(SiO[2], " 24 atoms")))
‐‐scatterplot‐param kind 0 \
‐‐scatterplot‐param retry 4 \
idx <‐ cut(x$value, seq(min(x$value), max(x$value),
length.out=n+1), labels=FALSE, include.lowest=TRUE)
‐‐scatterplot‐param diagnostic 1 \
plot(x$x, x$y, xlim=c(0,1), ylim=c(0,1), col=pal[idx], pch=16, cex=1)
abline(h=0, lty=3)
SiO2‐24atoms.poscar \
abline(0, 1, lty=1)
abline(v=0:3*ncol(f)/3+1, lty=2, col='green')
SiO2‐24atoms.enthalpies
abline(0.1, 1, lty=3,lwd=2)
# All corresponding quantities in a scatterplot table (removing Index and Step)
abline(‐0.1, 1, lty=3, lwd=2)
a <‐ readAnalysis('analysis.dat')
pairs(a[‐c(1,2)], pch='.', cex=4, col='blue')
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
STM4 for USPEX tutorial - Mario Valle - 10/12/2012
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12/12/2012
End of a nice day…
Thank you!
BTW, I’m mvalle@cscs.ch
Long Island sunset
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