Visualising results

AndreaMeo

1st Advanced VAMPIRE Workshop

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GenerateoutputfileswithVAMPIRE

Configuration files in VAMPIRE

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• Include statement in input fileconfig:atomsconfig:atoms-output-rate=1

• This will generate some files:> -rw-r--r--@ 1 andrea staff 1506 14 Sep 00:46 Py.mat> -rw-r--r-- 1 andrea staff 1786 14 Sep 00:49 input> -rw-r--r-- 1 andrea staff 6109 14 Sep 00:49 log> -rw-r--r-- 1 andrea staff 997 14 Sep 00:49 output> -rw-r--r-- 1 andrea staff 211958 14 Sep 00:49 atoms-coords.data> -rw-r--r-- 1 andrea staff 527 14 Sep 00:49 atoms-coords.meta> -rw-r--r-- 1 andrea staff 277816 14 Sep 00:49 spins-00000000.data> -rw-r--r-- 1 andrea staff 493 14 Sep 00:49 spins-00000000.meta> -rw-r--r-- 1 andrea staff 278227 14 Sep 00:49 spins-00000001.data> -rw-r--r-- 1 andrea staff 493 14 Sep 00:49 spins-00000001.meta

Configuration files in VAMPIRE

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• Execute vdc utility> /path/to/vdc/vdc

• This will generate some new files:

> -rw-r--r-- 1 andrea staff 202212 14 Sep 00:55 crystal.xyz> -rw-r--r-- 1 andrea staff 738018 14 Sep 00:55 spins-00000000.inc> -rw-r--r-- 1 andrea staff 738429 14 Sep 00:55 spins-00000001.inc> -rw-r--r-- 1 andrea staff 151 14 Sep 00:55 spins.ini> -rw-r--r-- 1 andrea staff 2906 14 Sep 00:55 spins.pov

crystal.xyz

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9747

Ag 1e-9 1e-9 1e-9Fe 1.775 1.775 1e-9Fe 1.775 1e-9 1.775Ag 1e-9 1.775 1.775Ag 3.55 1e-9 1e-9Fe 5.325 1.775 1e-9Ag 5.325 1e-9 1.775Ag 3.55 1.775 1.775

File containing crystal structure in xyz standard format

Number of atoms

Element,asdefinedinmaterial[1]:material-element=Ag

Atomiccoordinates

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Toolsforvisualisation

Tools for visualisation

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1. Gnuplot• Standard command-line tool that allows to generate 2D, 3D

and surface plots

• It’s quick and fast

• Can be used via script files

• Run on every platform

2. Povray• High quality tool for creating images Great and cool for spin

configurations and in general 3D plots à Suitable when youwant to publish

3. Rasmol, Jmol, Vesta, VMD (etc.)• Visualise crystal structure

Plotting 2D data with gnuplot

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# Inbashwecansortthedatainafilebasedonspecifickeys(-k):>sort -k 1g -k 3g output

#Enteringnuplot:> Gnuplot

#column3istheanglephi,column6isy-componentoftorque#Ingnuplot wecanhaveconditionalstatements:($1==0 ?$3:0/0):($6)

#Onceingnuplot,typethefollowingcommands

> plot ‘<sort -k 1g -k 3g output’ u($1==0?$3:0/0):($6) w l

FILE to plot COLUMNS to plot

PLOT with lines

Plotting 3D data with gnuplot

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• It is possible to visualise the spin configuration via gnuplot

• Spatial coordinates are stored in: atoms-coords.data• Spins coordinates are stored in: spins-(some zeros)#.data

• Combining the files is possible to generate a 3D plot

sp ”<paste atoms-coords.data spins-*.data” u 3:4:5:8 palette

sp ”<paste atoms-coords.data spins-*.data” u 3:4:5:6:7:8:8 w vector

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a) Web page for details, documentation and support:

www.povray.org

b) Download Povray from github repository:

https://github.com/POV-Ray/povray/tree/3.7-stable

c) To install look at “README.md” in “unix” directory in thegithub

Povray

> git clone https://github.com/POV-Ray/povray.git

#Otherwise download the zip file from github

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How to obtain and compile Povray

> cd unix/

> ./prebuild.sh

> cd ../

> ./configure COMPILED_BY="your name <email@address>"

> make

> make install

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How to compile Povray as NON-root

> ./configure –-prefix=/where/you/want/to/installCOMPILED_BY="your name <email@address>” -–without-libtiff NON_REDISTRIBUTABLE_BUILD=yes> make check

> cd unix/

> ./prebuild.sh

> cd ../

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Running Povray

> /path/to/vdc/vdc

> povray spins # render all snapshots in order

# or you can select only specific snapshots/ranges

> povray +KFI0 +KFF1 +A0.3 spins.pov

Initialframe

Finalframe

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Running Povray

# You can add some option as resolution of the image

> povray –W1600 –H1200 +A0.3 spins.pov

Resolution

# Although, you can change this, as well as theantialiasing in the spins.ini file

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Running Povray as NON-root

> /path/to/vdc/vdc

Whereyourexecutablehasbeen

createdSpecifypathto

“include”libraries

> /path/to/povray/unix/povray +L/path/to/prefix/include spins

spins.ini

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Width = 800Height = 600

Antialias = OnAntialias_Threshold = 0.3

Define some global parameter for povray

Resolution

Antialiasing

spins-00000000.inc

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spinm0(-49.7,-49.7,-4.43723,-0.484481,0.412277,0.771561,0.0741268,0.0741268,1)spinm1(-47.925,-49.7,-2.66223,0.853587,-0.413335,-0.317085,1,0.619498,0.619498)

File containing coords and spins to be input in povray

Spincoordinates

Materialnumberasdefinedinmaterialfilematerial[1]:…material[2]:…

Atomiccoordinates ColourinRGBformat

spins.pov – colours settings

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#version 3.5;#include "colors.inc"#include "metals.inc"#include "screen.inc"

File containing parameters and settings for executing povray

Declarecompatibilityversion

Colourpalettetobeused

spins.pov – global & camera settings

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global_settings { assumed_gamma 2.0 }

Backgroundcolour

background { color Gray30 }

Set_Camera(<CX,CY,CZ>, <LX,LY,LZ>, 15)

Cameralocation

Cameralookat

Cameraangle

spins.pov – camera settings

20Image from: “http://www.povray.org/documentation/3.7.0/r3_4.html#r3_4_2_1_1”

spins.pov – camera settings

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Set_Camera_Aspect(4,3)

Aspectratio

Set_Camera_Sky(<0,0,1>)

light_source { <2*CX, 2*CY, 2*CZ> color White}

Tiltsthecamera

Definepointlightsource

Locationoflightsource

Colouroflightsource

spins.pov – materials settings

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#declare sscale0=2.0; #declare rscale0=1.2;#declare cscale0=3.54;#declare cones0=0;#declare arrows0=1;#declare spheres0=1;#declare cubes0=0;#declare spincolors0=1;#declare spincolor0=pigment {color rgb < 0.1 0.1 0.1 >};

Declare parameters for each material defined in the material file

Parametersthatwillbeusedtocreatedifferent

shapes

spins.pov – materials settings

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#macro spinm0(cx,cy,cz,sx,sy,sz, cr,cg,cb)union{#if(spheres0) sphere {<cx,cy,cz>,0.5*rscale0} #end#if(cubes0) box {<cx-cscale0*0.5,cy-cscale0*0.5,cz-

cscale0*0.5>,<cx+cscale0*0.5,cy+cscale0*0.5,cz+cscale0*0.5>} #end#if(cones0) cone {<cx+0.5*sx*sscale0,cy+0.5*sy*sscale0,cz+0.5*sz*sscale0>,0.0

<cx-0.5*sx*sscale0,cy-0.5*sy*sscale0,cz-0.5*sz*sscale0>,sscale0*0.5} #end#if(arrows0) cylinder

{<cx+sx*0.5*sscale0,cy+sy*0.5*sscale0,cz+sz*0.5*sscale0>,<cx-sx*0.5*sscale0,cy-sy*0.5*sscale0,cz-sz*0.5*sscale0>,sscale0*0.12}cone {<cx+sx*0.5*1.6*sscale0,cy+sy*0.5*1.6*sscale0,cz+sz*0.5*1.6*sscale0>,sscale0*0.0 <cx+sx*0.5*sscale0,cy+sy*0.5*sscale0,cz+sz*0.5*sscale0>,sscale0*0.2} #end

#if(spincolors0) texture { pigment {color rgb <cr cg cb>}finish {reflection{ref} diffuse 1 ambient 0}}

#else texture { spincolor0 finish {reflection {ref} diffuse 1 ambient 0}} #end}#end

Declare parameters for each material defined in the material file

Examples – nice perspective views of spiral configurations

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Examples – top view of domains

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T = 5K

T = 50K

T = 300K

Examples – vortex spin structure

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Examples – crystal structure

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Examples – unit cell/crystal structure

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Image from: Daniel Meilak

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Thankyouforyoutime!