git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13900 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,45 +0,0 @@
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NOTE: This example requires the "Al99.eam.alloy" file.
|
||||
(It was not included in this directory because if its large size.)
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||||
As of 2012-11, I was able to obtain it here:
|
||||
http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
|
||||
Copy it to the directory containing this README file.
|
||||
------------------------------------------------------------------------
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||||
3D fractal test
|
||||
|
||||
Moltemplate is useful for building larger molecular structures from
|
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smaller pieces. Although this simulation is of no scientific value, thiss
|
||||
example illustrates how to build large (many-level) heirarchical objects
|
||||
(Serpinski cubes) using moltemplate. (This is also called a "Menger Sponge".)
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||||
|
||||
The files in this directory demonstrate a way to build a periodic lattice of
|
||||
3-dimensional Serpinski-cubes (with 3 levels of recursive self-similarity).
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||||
|
||||
In this example, the basic indivisible units are 4-atoms of Aluminum
|
||||
(arranged in a cubic FCC unit-cell for bulk Aluminum).
|
||||
This was an arbitrary choice. The resulting construct is not stable.
|
||||
(But it makes pretty movies while collapsing.)
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||||
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||||
To understand what is going on with this example, look at this file:
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||||
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||||
./moltemplate_files/elegant_inefficient_version/serpinski_cubes.lt
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||||
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||||
(This approach uses too much memory to be practical for large simulaions.
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||||
The version I actually use is here: ./moltemplate_files/serpinski_cubes.lt)
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||||
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||||
--- To build the system ---
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||||
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||||
Carry out the instructions in README_setup.sh,
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to generate the LAMMPS DATA file and input scripts you need:
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system.data, system.in.init, system.in.settings.
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(The run.in script contains references to these files.)
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||||
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||||
--- To run LAMMPS, try a command like: ---
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||||
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||||
lmp_mpi -i run.in
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||||
|
||||
or (if you have mpi installed)
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||||
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||||
mpirun -np 4 lmp_mpi -i run.in
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||||
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||||
This will create an ordinary LAMMPS dump file you can visualize with VMD
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traj.lammpstrj (See README_visualize.txt)
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@ -1,29 +0,0 @@
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# Use these commands to generate the LAMMPS input script and data file
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# (and other auxilliary files):
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||||
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||||
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# Create LAMMPS input files this way:
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cd moltemplate_files
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# run moltemplate
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moltemplate.sh -atomstyle full system.lt
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# This will generate various files with names ending in *.in* and *.data.
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# These files are the input files directly read by LAMMPS. Move them to
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# the parent directory (or wherever you plan to run the simulation).
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mv -f system.in* system.data ../
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# We will also need the "Al99.eam.alloy" file:
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#cp -f Al99.eam.alloy ../
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# This file was downloaded from:
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# http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
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||||
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||||
|
||||
# Optional:
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||||
# The "./output_ttree/" directory is full of temporary files generated by
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||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
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rm -rf output_ttree/
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||||
cd ../
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||||
@ -1,87 +0,0 @@
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||||
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||||
------- To view a lammps trajectory in VMD --------
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||||
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||||
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||||
1) Build a PSF file for use in viewing with VMD.
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This step works with VMD 1.9 and topotools 1.2.
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(Older versions, like VMD 1.8.6, don't support this.)
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||||
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||||
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||||
a) Start VMD
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b) Menu Extensions->Tk Console
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c) Enter:
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(I assume that the the DATA file is called "system.data")
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topo readlammpsdata system.data full
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animate write psf system.psf
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2)
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Later, to Load a trajectory in VMD:
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||||
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||||
Start VMD
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Select menu: File->New Molecule
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-Browse to select the PSF file you created above, and load it.
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(Don't close the window yet.)
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-Browse to select the trajectory file.
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If necessary, for "file type" select: "LAMMPS Trajectory"
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Load it.
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|
||||
---- A note on trajectory format: -----
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||||
If the trajectory is a DUMP file, then make sure the it contains the
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||||
information you need for pbctools (see below. I've been using this
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||||
command in my LAMMPS scripts to create the trajectories:
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||||
dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
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||||
|
||||
It's a good idea to use an atom_style which supports molecule-ID numbers
|
||||
so that you can assign a molecule-ID number to each atom. (I think this
|
||||
is needed to wrap atom coordinates without breaking molecules in half.)
|
||||
|
||||
Of course, you don't have to save your trajectories in DUMP format,
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||||
(other formats like DCD work fine) I just mention dump files
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||||
because these are the files I'm familiar with.
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||||
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||||
3) ----- Wrap the coordinates to the unit cell
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||||
(without cutting the molecules in half)
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||||
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||||
a) Start VMD
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||||
b) Load the trajectory in VMD (see above)
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||||
c) Menu Extensions->Tk Console
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||||
d) Try entering these commands:
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||||
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||||
pbc wrap -compound res -all
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pbc box
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----- Optional ----
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||||
Sometimes the solvent or membrane obscures the view of the solute.
|
||||
It can help to shift the location of the periodic boundary box
|
||||
To shift the box in the y direction (for example) do this:
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|
||||
pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
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pbc box -shiftcenterrel {0.0 0.15 0.0}
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||||
|
||||
Distances are measured in units of box-length fractions, not Angstroms.
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||||
|
||||
Alternately if you have a solute whose atoms are all of type 1,
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then you can also try this to center the box around it:
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||||
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||||
pbc wrap -sel type=1 -all -centersel type=2 -center com
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||||
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||||
4)
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||||
You should check if your periodic boundary conditions are too small.
|
||||
To do that:
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||||
select Graphics->Representations menu option
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||||
click on the "Periodic" tab, and
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click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
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||||
|
||||
5) Optional: If you like, change the atom types in the PSF file so
|
||||
that VMD recognizes the atom types, use something like:
|
||||
|
||||
sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
|
||||
sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
|
||||
sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
|
||||
|
||||
(If you do this, it might effect step 2 above.)
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||||
Binary file not shown.
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@ -1,64 +0,0 @@
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||||
# "AlCell" defines the 4-atom FCC unit cell
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||||
# of Aluminum (with a 4.05 angstrom spacing)
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||||
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||||
AlCell {
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||||
|
||||
# AtomID MolID(IGNORE!) AtomType Charge X Y Z
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||||
|
||||
write("Data Atoms") {
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||||
$atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000
|
||||
$atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025
|
||||
$atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025
|
||||
$atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000
|
||||
}
|
||||
|
||||
write_once("In Init") {
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||||
units metal
|
||||
atom_style full # <- Requires each atom has a MolID and Charge.
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||||
# This is not necessary. (Why use "full"?
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||||
# The "full" atom style is useful if you want to
|
||||
# mix the aluminum with other molecules later.
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||||
# Otherwise, just use "atom_style atomic", and
|
||||
# and remove the 2nd and 4th columns above.)
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||||
pair_style eam/alloy
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
pair_coeff * * Al99.eam.alloy Al
|
||||
}
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||||
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||||
write_once("Data Masses") {
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||||
@atom:Al 27.0
|
||||
}
|
||||
|
||||
} # AlCell
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||||
|
||||
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||||
|
||||
|
||||
|
||||
# Here is an alternate way to define AlCell
|
||||
# using "scale(4.05)" to select the lattice spacing:
|
||||
#
|
||||
#FccCell {
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||||
# write("Data Atoms") {
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||||
# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0
|
||||
# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5
|
||||
# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5
|
||||
# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0
|
||||
# }
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||||
# write_once("Data Masses") {
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||||
# @atom:Al 27.0
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||||
# }
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||||
# write_once("In Init") {
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||||
# units metal
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||||
# atom_style full
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||||
# pair_style eam/alloy
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||||
# }
|
||||
# write_once("In Settings") {
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||||
# pair_coeff * * Al99.eam.alloy Al
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||||
# }
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||||
#}
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||||
#
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||||
#AlCell = FccCell.scale(4.05)
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||||
#
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||||
@ -1,64 +0,0 @@
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||||
# "AlCell" defines the 4-atom FCC unit cell
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||||
# of Aluminum (with a 4.05 angstrom spacing)
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||||
|
||||
AlCell {
|
||||
|
||||
# AtomID MolID(IGNORE!) AtomType Charge X Y Z
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||||
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||||
write("Data Atoms") {
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||||
$atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000
|
||||
$atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025
|
||||
$atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025
|
||||
$atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000
|
||||
}
|
||||
|
||||
write_once("In Init") {
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||||
units metal
|
||||
atom_style full # <- Requires each atom has a MolID and Charge.
|
||||
# This is not necessary. (Why use "full"?
|
||||
# The "full" atom style is useful if you want to
|
||||
# mix the aluminum with other molecules later.
|
||||
# Otherwise, just use "atom_style atomic", and
|
||||
# and remove the 2nd and 4th columns above.)
|
||||
pair_style eam/alloy
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
pair_coeff * * Al99.eam.alloy Al
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:Al 27.0
|
||||
}
|
||||
|
||||
} # AlCell
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# Here is an alternate way to define AlCell
|
||||
# using "scale(4.05)" to select the lattice spacing:
|
||||
#
|
||||
#FccCell {
|
||||
# write("Data Atoms") {
|
||||
# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0
|
||||
# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5
|
||||
# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5
|
||||
# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0
|
||||
# }
|
||||
# write_once("Data Masses") {
|
||||
# @atom:Al 27.0
|
||||
# }
|
||||
# write_once("In Init") {
|
||||
# units metal
|
||||
# atom_style full
|
||||
# pair_style eam/alloy
|
||||
# }
|
||||
# write_once("In Settings") {
|
||||
# pair_coeff * * Al99.eam.alloy Al
|
||||
# }
|
||||
#}
|
||||
#
|
||||
#AlCell = FccCell.scale(4.05)
|
||||
#
|
||||
@ -1,34 +0,0 @@
|
||||
import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell
|
||||
|
||||
# This approach uses the "delete" command.
|
||||
# It works and it is elegant, but because the majority of atoms will be
|
||||
# deleted, (and because memory is allocated for all atoms, including
|
||||
# deleted atoms) this approach is not very memory efficient.
|
||||
|
||||
MengerCubeLvl1 {
|
||||
cells = new AlCell [3].move(0.00, 0.00, 4.05)
|
||||
[3].move(0.00, 4.05, 0.00)
|
||||
[3].move(4.05, 0.00, 0.00)
|
||||
delete cells[*][1][1]
|
||||
delete cells[1][*][1]
|
||||
delete cells[1][1][*]
|
||||
}
|
||||
|
||||
MengerCubeLvl2 {
|
||||
cells = new MengerCubeLvl1 [3].move(0.00, 0.00, 12.15)
|
||||
[3].move(0.00, 12.15, 0.00)
|
||||
[3].move(12.15, 0.00, 0.00)
|
||||
delete cells[*][1][1]
|
||||
delete cells[1][*][1]
|
||||
delete cells[1][1][*]
|
||||
}
|
||||
|
||||
MengerCubeLvl3 {
|
||||
cells = new MengerCubeLvl2 [3].move(0.00, 0.00, 36.45)
|
||||
[3].move(0.00, 36.45, 0.00)
|
||||
[3].move(36.45, 0.00, 0.00)
|
||||
delete cells[*][1][1]
|
||||
delete cells[1][*][1]
|
||||
delete cells[1][1][*]
|
||||
}
|
||||
|
||||
@ -1,34 +0,0 @@
|
||||
# Periodic boundary conditions:
|
||||
write_once("Data Boundary") {
|
||||
0.0 218.7 xlo xhi
|
||||
0.0 218.7 ylo yhi
|
||||
0.0 218.7 zlo zhi
|
||||
}
|
||||
|
||||
import "menger_cubes.lt"
|
||||
|
||||
cube_at_000 = new MengerCubeLvl3.move(0.0000, 0.0000, 0.0000)
|
||||
cube_at_100 = new MengerCubeLvl3.move(109.35, 0.0000, 0.0000)
|
||||
cube_at_010 = new MengerCubeLvl3.move(0.0000, 109.35, 0.0000)
|
||||
cube_at_001 = new MengerCubeLvl3.move(0.0000, 0.0000, 109.35)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
################################################################
|
||||
# The next command is not necessary:
|
||||
#
|
||||
create_var { $mol } # <-This forces all of the Al atoms in the crystal
|
||||
# # to share the same molecule ID number.
|
||||
# # Molecule ID numbers are not necessary. Ignore this.
|
||||
#
|
||||
@ -1,66 +0,0 @@
|
||||
import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell
|
||||
|
||||
# A Menger cube is a fractal which resembles a 3x3x3 Rubik's-cube. It has a
|
||||
# cube in each central face (and in the interior) removed. There are 3x3x3-7=20
|
||||
# remaining sub-cubes. Each of these 20 sub-cubes is a smaller MengerCube.
|
||||
# To build a MengerCube, you can list all 20 sub-cubes, or you can fill a
|
||||
# 3x3x3 cube with sub-cubes and delete the interior sub-cubes. (The later
|
||||
# approach is used in file "elegant_inefficient_version/menger_cubes.lt")
|
||||
|
||||
|
||||
|
||||
MengerCubeLvl1 {
|
||||
# Again, a Menger-cube is constructed of 20 smaller cube-shaped objects.
|
||||
# Here, the small cube-shaped objects are "AlCells" (defined in "al_cell.lt").
|
||||
# I could list out the positions of all 20 AlCells, (and this would be clearer
|
||||
# for the reader). However instead I built it from a combination of
|
||||
# two-dimensional and three-dimensional arrays of AlCells (explained below).
|
||||
|
||||
# The next command creates 12 AlCells (2x2x3) at:
|
||||
# (0.0, 0.0, 0.0), (0.0, 0.0, 4.05), (0.0, 0.0, 8.1)
|
||||
# (0.0, 8.1, 0.0), (0.0, 8.1, 4.05), (0.0, 8.1, 8.1)
|
||||
# (8.1, 8.1, 0.0), (8.1, 8.1, 4.05), (8.1, 8.1, 8.1)
|
||||
|
||||
cells_z = new AlCell [2].move(8.10, 0.00, 0.00)
|
||||
[2].move(0.00, 8.10, 0.00)
|
||||
[3].move(0.00, 0.00, 4.05)
|
||||
|
||||
# The next command creates 4 AlCells at: (0, 4.05, 0.0), (8.1, 4.05, 0.0),
|
||||
# (0, 4.05, 8.1), (8.1, 4.05, 8.1)
|
||||
|
||||
cells_xz = new AlCell.move(0.00, 4.05, 0.00) [2].move(8.10, 0.0, 0.0 )
|
||||
[2].move(0.0, 0.0, 8.10)
|
||||
|
||||
# The next command creates 4 AlCells at: (4.05, 0, 0.0), (4.05, 8.1, 0.0),
|
||||
# (4.05, 0, 8.1), (4.05, 8.1, 8.1)
|
||||
|
||||
cells_yz = new AlCell.move(4.05, 0.00, 0.00) [2].move(0.0, 8.10, 0.0 )
|
||||
[2].move(0.0, 0.0, 8.10)
|
||||
}
|
||||
|
||||
|
||||
|
||||
MengerCubeLvl2 {
|
||||
# Identical arrangement to MengerCube1 (with 3x larger length scales)
|
||||
cells_z = new MengerCubeLvl1 [2].move(24.3, 0.00, 0.00)
|
||||
[2].move(0.00, 24.3, 0.00)
|
||||
[3].move(0.00, 0.00, 12.15)
|
||||
cells_xz= new MengerCubeLvl1.move(0.0,12.15,0.0) [2].move(24.3, 0.0, 0.0 )
|
||||
[2].move(0.0, 0.0, 24.3)
|
||||
cells_yz= new MengerCubeLvl1.move(12.15,0.0,0.0) [2].move(0.0, 24.3, 0.0 )
|
||||
[2].move(0.0, 0.0, 24.3)
|
||||
}
|
||||
|
||||
|
||||
|
||||
MengerCubeLvl3 {
|
||||
# Identical arrangement to MengerCube2 (with 3x larger length scales)
|
||||
cells_z = new MengerCubeLvl2 [2].move(72.9, 0.00, 0.00)
|
||||
[2].move(0.00, 72.9, 0.00)
|
||||
[3].move(0.00, 0.00, 36.45)
|
||||
cells_xz= new MengerCubeLvl2.move(0.0,36.45,0.0) [2].move(72.9, 0.0, 0.0 )
|
||||
[2].move(0.0, 0.0, 72.9)
|
||||
cells_yz= new MengerCubeLvl2.move(36.45,0.0,0.0) [2].move(0.0, 72.9, 0.0 )
|
||||
[2].move(0.0, 0.0, 72.9)
|
||||
}
|
||||
|
||||
@ -1,34 +0,0 @@
|
||||
# Periodic boundary conditions:
|
||||
write_once("Data Boundary") {
|
||||
0.0 218.7 xlo xhi
|
||||
0.0 218.7 ylo yhi
|
||||
0.0 218.7 zlo zhi
|
||||
}
|
||||
|
||||
import "menger_cubes.lt"
|
||||
|
||||
cube_at_000 = new MengerCubeLvl3.move(0.0000, 0.0000, 0.0000)
|
||||
cube_at_100 = new MengerCubeLvl3.move(109.35, 0.0000, 0.0000)
|
||||
cube_at_010 = new MengerCubeLvl3.move(0.0000, 109.35, 0.0000)
|
||||
cube_at_001 = new MengerCubeLvl3.move(0.0000, 0.0000, 109.35)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
################################################################
|
||||
# The next command is not necessary:
|
||||
#
|
||||
create_var { $mol } # <-This forces all of the Al atoms in the crystal
|
||||
# # to share the same molecule ID number.
|
||||
# # Molecule ID numbers are not necessary. Ignore this.
|
||||
#
|
||||
@ -1,38 +0,0 @@
|
||||
# ------------------------------- Initialization Section --------------------
|
||||
|
||||
include system.in.init
|
||||
|
||||
# ------------------------------- Atom Definition Section -------------------
|
||||
|
||||
read_data system.data
|
||||
|
||||
# ------------------------------- Settings Section --------------------------
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# ------------------------------- Run Section -------------------------------
|
||||
#
|
||||
# Some of the run-settings below were stolen from:
|
||||
#
|
||||
# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression
|
||||
|
||||
# EQUILIBRATION
|
||||
reset_timestep 0
|
||||
timestep 0.001
|
||||
velocity all create 300 12345 mom yes rot no
|
||||
fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1
|
||||
|
||||
# Output files
|
||||
thermo 100
|
||||
thermo_style custom step ke pe press
|
||||
dump dCoords all custom 100 traj.lammpstrj id type x y z ix iy iz
|
||||
|
||||
run 20000
|
||||
|
||||
# Run for at least 10 picosecond (assuming 1 fs timestep)
|
||||
run 10000
|
||||
|
||||
|
||||
######################################
|
||||
# SIMULATION DONE
|
||||
print "All done"
|
||||
Reference in New Issue
Block a user