uspex 2012 cecam workshop –22/10/2012 how to analyze...

22/10/2012

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How to analyze thousands of complex crystal structures in a minute

Mario ValleUSPEX 2012 CECAM workshop – 22/10/2012

Tutorial planSTM4 components

and structure

CrystalFpSTM4

components

CrystalFpanalysis

examples

AVS/Expressconcepts

STM4quick tour

CrystalFpbatch

Logistic information

Login on the tutorial machines with:

Username: Password:

Test data files are under:

~tutoadmin/CSCSlib/stm4-examples/data

Run STM4 with:

$ cd ~tutoadmin/CSCSlib $ ./go

STM4 for USPEX tutorial - Mario Valle - 22/10/2012

Ready? Go!STM4 components

and structure

CrystalFpSTM4

components

CrystalFpanalysis

examples

AVS/Expressconcepts

STM4quick tour

CrystalFpbatch

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STM4 is a frameworkfor the development of

unusual and enhanced techniquesfor chemistry visualization

Start STM4 (and 2″ tutorial) Launch AVS/Express (with STM4 included):

$ express (Linux)

C:\> cd CSCSlibC:\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 functional areas

Libraries

Build areaView resultsModules

GUI

Viewer control

Access to the STM4 library

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STM4 modules (look at them)

A B C D E F G H I J K

A. Readers and writers: chemical formats, screenshots and moviesB. Bonds related modules: compute, count and editC. Modules that compute various derived structuresD. Atoms selection by various criteriaE. Trajectory related modulesF. Crystallography support modules: symmetries, replications, etc.G. Visualization of volumetric data like Gaussian cubesH. Structure display and related graphical objectsI. Probe, interaction and measurementsJ. Ready to run applications (plus display of the STM4 version)K. Specialized modules (like USPEX output analysis applications)

The prebuilt MolDisplayApp

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 MolDisplayApp

Another application example


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STM4 data types


Molecule Data Type Standard AVS Field

Geometries

Screen Image

DisplayParameters

STM4 module documentation

STM4 resources

STM4 main pages http://mariovalle.name/STM4/

The STM4 modules documentationhttp://mariovalle.name/STM4/doc/STM4/

STM4 downloadhttp://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 coursehttp://mariovalle.name/AVS/introduction-to-xp.html

A (marketing) brochure on AVS/Expresshttp://www.avs.com/software/soft_t/avsxps.html


New topicSTM4 components

and structure

CrystalFpSTM4

components

CrystalFpanalysis

examples

AVS/Expressconcepts

STM4quick tour

CrystalFpbatch

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STM4 architecture has… …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

AVS/Express components

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Data Viewer

Module GUI

Editors (access to rendering parameters)

Status panel

Quick access

Viewer

Default library


Libraries


Viz techniques

More than 500 visualization techniques available

Readers available for a broad range of file formats

AVS/Express prototyping support helps to find the most useful technique

Any technique can be adapted to suit specific user requirements

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Network Editor: the build areaApplications are built dragging modules from the libraries to the Network Editor

Network Editor

Try to find the AVS/Express parts

Go to: Libraries Examples

Instantiate: Visualization OrthosliceBy dragging it to the empty area


Dataflow architecture



Wait

Wait Wait

Wait

Wait

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Wait

Wait

Wait

Wait

Enter filename



Execute

Wait

Wait

Wait

Valid data



Wait

Wait

Wait

Valid dataNot valid

data



Wait

Wait

Enter filename

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Wait

Valid dataValid data

Execute



Execute


The result of this application Speak to the AVS/Express core

Object Manager

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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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Various AVS/Express editions


Developer Edition Everything you need Modules to develop applications Standard modules can be opened

Visualization Edition Some modules not available Cannot create runtimes Cost less No differences if you are

an End User

STM4 works with both editionsSTM4 for USPEX tutorial - Mario Valle - 22/10/2012

Some AVS/Express resources

AVS homepage: http://www.avs.com/

Official documentation: http://help.avs.com/Express/

AVS forum: http://forum.avs.com/

AVS/Express built‐in examples

Visualization techniques book (in the AVS/Express manuals)

International AVS Center (IAC): http://www.iavsc.org/

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/

A user level AVS/Express course:http://mariovalle.name/AVS/introduction‐to‐xp.html


and structure

CrystalFpSTM4

components

CrystalFpanalysis

examples

AVS/Expressconcepts

STM4quick tour

CrystalFpbatch

STM4 modules

A B C D E F G H I J K

A. Readers and writers: chemical formats, screenshots and moviesB. Bonds related modules: compute, count and editC. Modules that compute various derived structuresD. Atoms selection by various criteriaE. Trajectory related modulesF. Crystallography support modules: symmetries, replications, etc.G. Visualization of volumetric data like Gaussian cubesH. Structure display and related graphical objectsI. Probe, interaction and measurementsJ. Ready to run applications (plus display of the STM4 version)K. Specialized modules (like USPEX output analysis applications)

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Pre-built applications

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

MolDisplayApp

Move to CrystalDisplay Add tetrahedra

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Add title, logo and background Measure a structure

Readers/writers

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 ray-

tracing

STM4 – formats supported


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Two static structures Display Rendering of chemical structures and other graphical objects.

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.

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.

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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).

Interactivity (probe & measure)

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 a structure

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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.

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.

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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.

Access volumetric data Volume rendering

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Crystallography support

Unit cells, periodic lattices and symmetries support. 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

the atoms coordinates. Crop Structure Inside a geometric shape (cube, sphere, tube,…) Crop From Plane Remove atoms that dist more than a given value

from a plane. Miller Plane Crop the atoms using the plane identified by given

Miller indices. Draw Polyhedra Draw polyhedra around selected atoms X Ray Structure Factor Compute and display simplified X-Ray

structure factors. Remove Border Atoms Remove atoms that bonds with atoms

outside the unit cell. Merge Unit Cell Apply the unit cell of one structure to another one.

Crop Structure

Find symmetries Fermi surfaces

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Find enthalpy transitions Convex-hull method support


and structure

CrystalFpSTM4

components

CrystalFpanalysis

examples

AVS/Expressconcepts

STM4quick tour

CrystalFpbatch

CrystalFp applications

CrystalFp no energy

CrystalFp with energy

CrystalFp with energyand energy landscape


Secret fantastic newCrystalFp version

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Load the structure file Load the energy file

Initialize CrystalFp, load data Compute fingerprints & distances

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Adjust grouping (if needed) Analyze results

Build scatterplot Scatterplot diagnostics

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Build energy landscape Structure alignment

Your turn!STM4 components

and structure

CrystalFpSTM4

components

CrystalFpanalysis

examples

AVS/Expressconcepts

STM4quick tour

CrystalFpbatch

Test with your data

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and structure

CrystalFpSTM4

components

CrystalFpanalysis

examples

AVS/Expressconcepts

STM4quick tour

CrystalFpbatch

Scripts differences

On WindowsRelease\cfp.exe ^‐‐verbose=1 ^‐‐elements=“Si O” ^SiO2‐24atoms.poscar ^SiO2‐24atoms.enthalpies

Script.bat

On Linux./cfp \

‐‐verbose=1 \‐‐elements=“Si O” \SiO2‐24atoms.poscar \SiO2‐24atoms.enthalpies

Script.sh


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

‐p ‐‐peak‐size (required argument)Peak smearing size

...

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


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Visualize results using Rsource('readers.r')

# Read sorted distances and display on a log‐log chart

s <‐ readSortedDist('sorted.dat')

plot(s, type='l', log='xy', xlab='Distance', ylab='Cumulative frequency',main=bquote(paste(SiO[2], " 24 atoms")))

# 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

f <‐ readFp('fp.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")))

plot(f[25,], type='s', xlab='Distance', ylab='Fingerprint value',main=bquote(paste(SiO[2], " 24 atoms")))

abline(h=0, lty=3)

abline(v=0:3*ncol(f)/3+1, lty=2, col='green')

# All corresponding quantities in a scatterplot table (removing Index and Step)

a <‐ readAnalysis('analysis.dat')

pairs(a[‐c(1,2)], pch='.', cex=4, col='blue')


It does also scatterplots!./cfp \

‐‐end‐step=50 \‐‐verbose=3 \‐‐elements="Si O" \‐‐fingerprint‐method=0 \‐‐distance‐method=0 \‐‐grouping‐method=1 \‐‐grouping‐threshold=0.05 \‐‐remove‐dupl=map.dat \‐‐scatterplot \‐‐scatterplot‐file=scatterplot.dat \‐‐diagnostic‐file=diagnostic.dat \‐‐scatterplot‐param iterations 200 \‐‐scatterplot‐param retry 4 \‐‐scatterplot‐param kind 0 \‐‐scatterplot‐param iterations 200 \‐‐scatterplot‐param retry 4 \‐‐scatterplot‐param kind 0 \‐‐scatterplot‐param diagnostic 1 \SiO2‐24atoms.poscar \SiO2‐24atoms.enthalpies


source('readers.r')

# Prepare the color palette

n <‐ 256

pal <‐ heat.colors(n)

# 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)

# Output the corresponding diagnostic chart

x <‐ readScatterplot('diagnostic.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(0,1), ylim=c(0,1), col=pal[idx], pch=16, cex=1)

abline(0, 1, lty=1)

abline(0.1, 1, lty=3,lwd=2)

abline(‐0.1, 1, lty=3, lwd=2)

End of a nice day…

Thank you!BTW, I’m [email protected]

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uspex 2012 cecam workshop –22/10/2012 how to analyze...

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