Merge pull request #36 from lammpstutorials/improve-tutorial-5

Improve tutorial 5

Author: simongravelle

figures/SIO-charge.png

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+# LAMMPS Tutorial manifest file. This file determines what is downloaded when.
+# comments start with a # as the first character.
+# comments and empty lines are ignored
+##############################################################################
+# 1) input file templates and data files
+# the first file will be automatically loaded
+decorate.lmp
+deform.lmp
+reaxCHOFe.inc
+relax.lmp
+silica.data
+
+# 2) solution files
+# only downloaded on request
+decorate-H.histo
+decorate.lmp
+decorate.log
+decorate-O.histo
+decorate.png
+decorate-Si.histo
+decorate.species
+deform.data
+deform.ipynb
+deform.lmp
+deform.log
+deform-mod.data
+deform-O.histo
+deform.png
+deform-Si.histo
+deform.species
+reaxCHOFe.inc
+relax.data
+relax.ipynb
+relax.lmp
+relax.log
+relax-O.histo
+relax.png
+relax-Si.histo
+relax.species
+silica.data
+
+# 3) support files
+

figures/SIO-deformed-charge.png

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+
+units real
+atom_style full
+
+read_data deform-mod.data
+displace_atoms all move −12 0 0 # optional
+
+pair_style reaxff NULL safezone 3.0 mincap 150
+pair_coeff * * reaxCHOFe.inc Si O H
+fix myqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400

figures/SIO-distribution.png

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+
+units real
+atom_style full
+
+read_data relax.data
+
+pair_style reaxff NULL safezone 3.0 mincap 150
+pair_coeff * * reaxCHOFe.inc Si O
+fix myqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
+
+group grpSi type Si
+group grpO type O
+variable qSi equal charge(grpSi)/count(grpSi)
+variable qO equal charge(grpO)/count(grpO)
+variable vq atom q
+
+thermo 200
+thermo_style custom step temp etotal press vol v_qSi v_qO
+dump viz all image 100 myimage-*.ppm q &
+  type shiny 0.1 box no 0.01 view 180 90 zoom 2.3 size 1200 500
+dump_modify viz adiam Si 2.6 adiam O 2.3 backcolor white &
+  amap -1 2 ca 0.0 3 min royalblue 0 green max orangered

files/tutorial5/.manifest

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+
+units real
+atom_style full
+
+read_data silica.data

files/tutorial5/decorate.lmp

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+# Histogrammed data for fix myhis3
+# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
+# Bin Coord Count Count/Total