git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13826 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
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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.)
|
||||
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.
|
||||
------------------------------------------------------------------------
|
||||
3D fractal test
|
||||
|
||||
Moltemplate is useful for building larger molecular structures from
|
||||
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".)
|
||||
|
||||
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).
|
||||
|
||||
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.)
|
||||
|
||||
To understand what is going on with this example, look at this file:
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||||
|
||||
./moltemplate_files/elegant_inefficient_version/serpinski_cubes.lt
|
||||
|
||||
(This approach uses too much memory to be practical for large simulaions.
|
||||
The version I actually use is here: ./moltemplate_files/serpinski_cubes.lt)
|
||||
|
||||
--- To build the system ---
|
||||
|
||||
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.)
|
||||
|
||||
--- To run LAMMPS, try a command like: ---
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||||
|
||||
lmp_mpi -i run.in
|
||||
|
||||
or (if you have mpi installed)
|
||||
|
||||
mpirun -np 4 lmp_mpi -i run.in
|
||||
|
||||
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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||||
29
tools/moltemplate/examples/misc_examples/menger_sponge/README_setup.sh
Executable file
29
tools/moltemplate/examples/misc_examples/menger_sponge/README_setup.sh
Executable file
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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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||||
|
||||
|
||||
# Create LAMMPS input files this way:
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||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh -atomstyle full system.lt
|
||||
|
||||
# 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
|
||||
# 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 ../
|
||||
# This file was downloaded from:
|
||||
# http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
|
||||
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
@ -0,0 +1,87 @@
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||||
|
||||
------- To view a lammps trajectory in VMD --------
|
||||
|
||||
|
||||
1) Build a PSF file for use in viewing with VMD.
|
||||
|
||||
This step works with VMD 1.9 and topotools 1.2.
|
||||
(Older versions, like VMD 1.8.6, don't support this.)
|
||||
|
||||
|
||||
a) Start VMD
|
||||
b) Menu Extensions->Tk Console
|
||||
c) Enter:
|
||||
|
||||
(I assume that the the DATA file is called "system.data")
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||||
|
||||
topo readlammpsdata system.data full
|
||||
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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||||
|
||||
Start VMD
|
||||
Select menu: File->New Molecule
|
||||
-Browse to select the PSF file you created above, and load it.
|
||||
(Don't close the window yet.)
|
||||
-Browse to select the trajectory file.
|
||||
If necessary, for "file type" select: "LAMMPS Trajectory"
|
||||
Load it.
|
||||
|
||||
---- A note on trajectory format: -----
|
||||
If the trajectory is a DUMP file, then make sure the it contains the
|
||||
information you need for pbctools (see below. I've been using this
|
||||
command in my LAMMPS scripts to create the trajectories:
|
||||
|
||||
dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
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,
|
||||
(other formats like DCD work fine) I just mention dump files
|
||||
because these are the files I'm familiar with.
|
||||
|
||||
3) ----- Wrap the coordinates to the unit cell
|
||||
(without cutting the molecules in half)
|
||||
|
||||
a) Start VMD
|
||||
b) Load the trajectory in VMD (see above)
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||||
c) Menu Extensions->Tk Console
|
||||
d) Try entering these commands:
|
||||
|
||||
pbc wrap -compound res -all
|
||||
pbc box
|
||||
|
||||
----- Optional ----
|
||||
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:
|
||||
|
||||
pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
|
||||
pbc box -shiftcenterrel {0.0 0.15 0.0}
|
||||
|
||||
Distances are measured in units of box-length fractions, not Angstroms.
|
||||
|
||||
Alternately if you have a solute whose atoms are all of type 1,
|
||||
then you can also try this to center the box around it:
|
||||
|
||||
pbc wrap -sel type=1 -all -centersel type=2 -center com
|
||||
|
||||
4)
|
||||
You should check if your periodic boundary conditions are too small.
|
||||
To do that:
|
||||
select Graphics->Representations menu option
|
||||
click on the "Periodic" tab, and
|
||||
click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
|
||||
|
||||
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.)
|
||||
Binary file not shown.
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@ -0,0 +1,64 @@
|
||||
# "AlCell" defines the 4-atom FCC unit cell
|
||||
# of Aluminum (with a 4.05 angstrom spacing)
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||||
|
||||
AlCell {
|
||||
|
||||
# AtomID MolID(IGNORE!) AtomType Charge X Y Z
|
||||
|
||||
write("Data Atoms") {
|
||||
$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") {
|
||||
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
|
||||
# }
|
||||
#}
|
||||
#
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||||
#AlCell = FccCell.scale(4.05)
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||||
#
|
||||
@ -0,0 +1,64 @@
|
||||
# "AlCell" defines the 4-atom FCC unit cell
|
||||
# of Aluminum (with a 4.05 angstrom spacing)
|
||||
|
||||
AlCell {
|
||||
|
||||
# AtomID MolID(IGNORE!) AtomType Charge X Y Z
|
||||
|
||||
write("Data Atoms") {
|
||||
$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") {
|
||||
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)
|
||||
#
|
||||
@ -0,0 +1,34 @@
|
||||
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][*]
|
||||
}
|
||||
|
||||
@ -0,0 +1,34 @@
|
||||
# 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.
|
||||
#
|
||||
@ -0,0 +1,66 @@
|
||||
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)
|
||||
}
|
||||
|
||||
@ -0,0 +1,34 @@
|
||||
# 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.
|
||||
#
|
||||
@ -0,0 +1,38 @@
|
||||
# ------------------------------- 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"
|
||||
@ -0,0 +1,23 @@
|
||||
Description:
|
||||
|
||||
This is a simulation of pyramid-shaped objects resting on an immobile surface
|
||||
(resembling graphene). Each pyramid is built from spherical particles stacked
|
||||
like cannon-balls, or stacked fruit. Ordinarily, the stack does not move
|
||||
because the particles at the ground layer are immobilized. However,
|
||||
given an initial (small) perturbation the pyramids collapse in an avalanche.
|
||||
|
||||
(In this example, the perturbation is due to shock because we (intentionally)
|
||||
did not minimize the system before starting the simulation. This shock
|
||||
causes an avalanche to occur approximately 5000 timesteps later.)
|
||||
|
||||
The particles roll down the pyramid and bounce off the "ground". The bouncing
|
||||
is due to a repulsive external force which is added artificially.
|
||||
(See the "run.in" file.) The simulation looks weird without something
|
||||
to bounce off of. So I added a graphene surface at the bottom as scenery.
|
||||
(It does not exert any force on the atoms.)
|
||||
|
||||
(Random comment: This could be a fun example to illustrate the Boltzmann
|
||||
distribution. Because there is no damping, in a small region, I'm guessing
|
||||
the particle heights should eventually approach the Boltzmann distribution
|
||||
for some temperature consistent with the initial potential energy of the
|
||||
system.)
|
||||
@ -0,0 +1,28 @@
|
||||
------- A note on building the graphene sheet in VMD: ------
|
||||
|
||||
Probably you can ignore these instructions.
|
||||
These instructions are not necessary for this example to run.
|
||||
|
||||
This example contains several pyramid shaped objects resting on a surface
|
||||
made of graphene. The instructions in this file explain how to build the
|
||||
graphene (representing the "ground") using VMD instead of with moltemplate.
|
||||
Why do this?
|
||||
VMD can create graphene sheets with bonds connecting neighboring carbon atoms,
|
||||
(which looks more pretty). However, as of 2013-4-29, moltemplate currently
|
||||
can not generate these bonds. It does not matter physically in this case,
|
||||
because the graphene sheet used here does not move. It is only used as
|
||||
scenery, to graphically represent the ground surface.
|
||||
|
||||
Select "Extensions"->"Modeling"->"Carbon Nanotube Builder"
|
||||
Build a graphene sheet of size 39.8 x 39.8 (units: nm)
|
||||
400.3358398 399.876008
|
||||
(try to use a size compatible with the periodic boundaries)
|
||||
Select "Extensions"->"Tk Console", and type
|
||||
display backgroundgradient on
|
||||
|
||||
Note: If you want to do this, before you run moltemplate, you may want to delete
|
||||
the sections of the "system.lt" file (located in "moltemplate_files")
|
||||
which define the graphene wall. Instead create the graphene data file
|
||||
in VMD. You will have to manually merge the data file for graphene
|
||||
with the data file for the pyramids created by moltemplate,
|
||||
(taking care to avoid overlapping atom-id numbers).
|
||||
23
tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_setup.sh
Executable file
23
tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README_setup.sh
Executable file
@ -0,0 +1,23 @@
|
||||
# Use these commands to generate the LAMMPS input script and data file
|
||||
# (and other auxilliary files):
|
||||
|
||||
|
||||
# Create LAMMPS input files this way:
|
||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh system.lt
|
||||
|
||||
# This will generate various files with names ending in *.in* and *.data.
|
||||
# These files are the input files directly read by LAMMPS. Move them to
|
||||
# the parent directory (or wherever you plan to run the simulation).
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
@ -0,0 +1,76 @@
|
||||
------- To view a lammps trajectory in VMD --------
|
||||
|
||||
|
||||
1) Build a PSF file for use in viewing with VMD.
|
||||
|
||||
This step works with VMD 1.9 and topotools 1.2.
|
||||
(Older versions, like VMD 1.8.6, don't support this.)
|
||||
|
||||
|
||||
a) Start VMD
|
||||
b) Menu Extensions->Tk Console
|
||||
c) Enter:
|
||||
|
||||
(I assume that the the DATA file is called "system.data")
|
||||
|
||||
topo readlammpsdata system.data full
|
||||
animate write psf system.psf
|
||||
|
||||
2)
|
||||
|
||||
Later, to Load a trajectory in VMD:
|
||||
|
||||
Start VMD
|
||||
Select menu: File->New Molecule
|
||||
-Browse to select the PSF file you created above, and load it.
|
||||
(Don't close the window yet.)
|
||||
-Browse to select the trajectory file.
|
||||
If necessary, for "file type" select: "LAMMPS Trajectory"
|
||||
Load it.
|
||||
|
||||
---- A note on trajectory format: -----
|
||||
If the trajectory is a DUMP file, then make sure the it contains the
|
||||
information you need for pbctools (see below. I've been using this
|
||||
command in my LAMMPS scripts to create the trajectories:
|
||||
|
||||
dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
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,
|
||||
(other formats like DCD work fine) I just mention dump files
|
||||
because these are the files I'm familiar with.
|
||||
|
||||
3) ----- Wrap the coordinates to the unit cell
|
||||
(without cutting the molecules in half)
|
||||
|
||||
a) Start VMD
|
||||
b) Load the trajectory in VMD (see above)
|
||||
c) Menu Extensions->Tk Console
|
||||
d) Try entering these commands:
|
||||
|
||||
pbc wrap -compound res -all
|
||||
pbc box
|
||||
|
||||
----- Optional ----
|
||||
To shift the box by a fraction in the x direction (for example)
|
||||
do this:
|
||||
|
||||
pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 }
|
||||
pbc box -shiftcenterrel {-0.50 -0.52 0.0 }
|
||||
|
||||
# Alternately if you have a solute whose atoms are all of type 1,
|
||||
# then you can also try this to center the box around it:
|
||||
|
||||
pbc wrap -sel type=1 -all -centersel type=2 -center com
|
||||
|
||||
4) 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.)
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 86 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 89 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 96 KiB |
@ -0,0 +1,15 @@
|
||||
# This directory contains moltemplate files for the "Pyramids of Giza" example.
|
||||
# (Note: the ground lattice work that appears in some images was not generated
|
||||
# by moltemplate. Moltemplate can not currently create bonded periodic
|
||||
# structures as of 2013-4-04. Those were generated by topotools.)
|
||||
#
|
||||
# To run moltemplate, use:
|
||||
|
||||
moltemplate.sh system.lt
|
||||
|
||||
# This will generate:system.data, system.in, system.in.init, system.in.settings
|
||||
#
|
||||
# The output_ttree/ directory will contain files like "Data Atoms", "Data Bonds"
|
||||
# which contain the corresponding structures of the system.data file.
|
||||
# (This might make it slightly easier to combine them with atom data and
|
||||
# bond data generated by other programs, such as topotools, for example.)
|
||||
@ -0,0 +1,61 @@
|
||||
# This file contains a unit cell for building graphene and nanotubes
|
||||
#
|
||||
#
|
||||
# The 4AtomRectCellXY "molecule" defined below is a reactangular unit cell
|
||||
# for hexagonal tesselations in 2-dimensions. (See "graphene_unit_cell.jpg")
|
||||
# Surfaces constructed with this unit cell can be flat or curved into tubes.
|
||||
# The distance between nearest-neighbor carbon atoms (ie the length of a
|
||||
# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms.
|
||||
#
|
||||
# d = length of each hexagon's side = 1.42 Angstroms
|
||||
# L = length of each hexagon = 2*d = 2.84 Angstroms
|
||||
# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms
|
||||
# 2w = width of hexagon rows = 3*l = 4.26 Angstroms
|
||||
#
|
||||
# Consequently, the Lattice-cell vectors for singe-layer graphene are:
|
||||
# (2.4595121467478, 0, 0) (aligned with X axis)
|
||||
# (0, 4.26, 0) (aligned with Y axis)
|
||||
# So, to build a sheet of graphite, you could use:
|
||||
# sheet = new Graphene/4AtomRectCellXY [10].move(2.4595121467478, 0, 0)
|
||||
# [10].move(0, 4.26, 0)
|
||||
|
||||
|
||||
|
||||
|
||||
Graphene {
|
||||
|
||||
4AtomRectCellXY
|
||||
{
|
||||
# atomID molID atomType charge x y z
|
||||
write("Data Atoms") {
|
||||
$atom:C11 $mol:... @atom:../C 0.0 0.61487803668695 0.71 0.0
|
||||
$atom:C21 $mol:... @atom:../C 0.0 1.84463411006085 1.42 0.0
|
||||
$atom:C12 $mol:... @atom:../C 0.0 0.61487803668695 3.55 0.0
|
||||
$atom:C22 $mol:... @atom:../C 0.0 1.84463411006085 2.84 0.0
|
||||
}
|
||||
}
|
||||
|
||||
# Now define properties of the Carbon graphene atom
|
||||
|
||||
write_once("In Init") {
|
||||
pair_style hybrid lj/cut 9.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:C 12.0
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# i j epsilon sigma
|
||||
pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407
|
||||
|
||||
# These Lennard-Jones parameters come from
|
||||
# R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus,
|
||||
# Chem Phys Lett, 348:187 (2001)
|
||||
|
||||
# Define a group consisting of only carbon atoms in graphene molecules
|
||||
group gGraphene type @atom:C
|
||||
}
|
||||
|
||||
} # Graphene
|
||||
|
||||
@ -0,0 +1,21 @@
|
||||
import "graphene.lt"
|
||||
|
||||
# -------------- graphene sheet -----------------
|
||||
|
||||
# Notes:
|
||||
# Hexagonal lattice with:
|
||||
# l = length of each hexagonal side = 1.42 Angstroms
|
||||
# L = length of each hexagon = 2*l = 2.84 Angstroms
|
||||
# W = width of each hexagon = 2*l*sqrt(3)/2 ~= 2.4595121467478 Angstroms
|
||||
# 2w = width of hexagon rows = 3.0*l = 4.26 Angstroms
|
||||
|
||||
|
||||
GrapheneWall {
|
||||
|
||||
unitcells = new Graphene/4AtomRectCellXY [163].move(2.456, 0, 0)
|
||||
[94].move(0, 4.254, 0)
|
||||
|
||||
# (Note: I fudged the spacing slightly to make it line up better with the
|
||||
# lattice spacing for graphene generated by VMD's graphene builder.)
|
||||
}
|
||||
|
||||
@ -0,0 +1,283 @@
|
||||
# Brick is a very simple molecule containing one "atom".
|
||||
# "ImmobileBrick" and "GoldBrick" are identical to "Brick" but are
|
||||
# given different atom types. (This makes it easier to put them in
|
||||
# different groups and apply different LAMMPS "fixes" to them.)
|
||||
|
||||
Brick {
|
||||
|
||||
# atomID molID atomType charge x y z
|
||||
write("Data Atoms") {
|
||||
$atom $mol @atom 0.0 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom 1.0
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6)
|
||||
#
|
||||
# i j eps sig
|
||||
pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
group gMobile type @atom
|
||||
# (Atoms of this type belong to the "gMobile" group)
|
||||
}
|
||||
|
||||
write_once("In Init") {
|
||||
atom_style full
|
||||
units lj
|
||||
pair_style lj/cut 1.0
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
#We want to stack "Brick"s the same way a green-grocer sometimes stack apples:
|
||||
#Place the apples at the base an square lattice of apples at the base.
|
||||
#The apples in the next layer up are placed in between the 4 apples beneath them.
|
||||
#Each new layer is smaller and placed above the previous layer at a height
|
||||
#of sigma / sqrt(2), where "sigma" is the diameter of each spherical "Brick".
|
||||
#We will artificially hold the apples at the base in place
|
||||
#(to keep the entire stack from collapsing).
|
||||
#
|
||||
# The lines below were generated from the following python loop:
|
||||
#
|
||||
#from math import *
|
||||
#N=50
|
||||
#s=1.0
|
||||
#for i in range(0,N):
|
||||
# print(" layer"+str(i)+" = new Brick.move("+str(-(N-(i+1))*s*0.5)+","+
|
||||
# str(-(N-(i+1))*s*0.5)+","+str(i*s/sqrt(2))+") ["+str(N-i)+"].move("+
|
||||
# str(s)+",0,0) ["+str(N-i)+"].move(0,"+str(s)+",0)")
|
||||
|
||||
|
||||
PyramidKhufu {
|
||||
layer0 = new ImmobileBrick.move(-24.5,-24.5,0.0) [50].move(1.0,0,0) [50].move(0,1.0,0)
|
||||
layer1 = new Brick.move(-24.0,-24.0,0.707106781187) [49].move(1.0,0,0) [49].move(0,1.0,0)
|
||||
layer2 = new Brick.move(-23.5,-23.5,1.41421356237) [48].move(1.0,0,0) [48].move(0,1.0,0)
|
||||
layer3 = new Brick.move(-23.0,-23.0,2.12132034356) [47].move(1.0,0,0) [47].move(0,1.0,0)
|
||||
layer4 = new Brick.move(-22.5,-22.5,2.82842712475) [46].move(1.0,0,0) [46].move(0,1.0,0)
|
||||
layer5 = new Brick.move(-22.0,-22.0,3.53553390593) [45].move(1.0,0,0) [45].move(0,1.0,0)
|
||||
layer6 = new Brick.move(-21.5,-21.5,4.24264068712) [44].move(1.0,0,0) [44].move(0,1.0,0)
|
||||
layer7 = new Brick.move(-21.0,-21.0,4.94974746831) [43].move(1.0,0,0) [43].move(0,1.0,0)
|
||||
layer8 = new Brick.move(-20.5,-20.5,5.65685424949) [42].move(1.0,0,0) [42].move(0,1.0,0)
|
||||
layer9 = new Brick.move(-20.0,-20.0,6.36396103068) [41].move(1.0,0,0) [41].move(0,1.0,0)
|
||||
layer10 = new Brick.move(-19.5,-19.5,7.07106781187) [40].move(1.0,0,0) [40].move(0,1.0,0)
|
||||
layer11 = new Brick.move(-19.0,-19.0,7.77817459305) [39].move(1.0,0,0) [39].move(0,1.0,0)
|
||||
layer12 = new Brick.move(-18.5,-18.5,8.48528137424) [38].move(1.0,0,0) [38].move(0,1.0,0)
|
||||
layer13 = new Brick.move(-18.0,-18.0,9.19238815543) [37].move(1.0,0,0) [37].move(0,1.0,0)
|
||||
layer14 = new Brick.move(-17.5,-17.5,9.89949493661) [36].move(1.0,0,0) [36].move(0,1.0,0)
|
||||
layer15 = new Brick.move(-17.0,-17.0,10.6066017178) [35].move(1.0,0,0) [35].move(0,1.0,0)
|
||||
layer16 = new Brick.move(-16.5,-16.5,11.313708499) [34].move(1.0,0,0) [34].move(0,1.0,0)
|
||||
layer17 = new Brick.move(-16.0,-16.0,12.0208152802) [33].move(1.0,0,0) [33].move(0,1.0,0)
|
||||
layer18 = new Brick.move(-15.5,-15.5,12.7279220614) [32].move(1.0,0,0) [32].move(0,1.0,0)
|
||||
layer19 = new Brick.move(-15.0,-15.0,13.4350288425) [31].move(1.0,0,0) [31].move(0,1.0,0)
|
||||
layer20 = new Brick.move(-14.5,-14.5,14.1421356237) [30].move(1.0,0,0) [30].move(0,1.0,0)
|
||||
layer21 = new Brick.move(-14.0,-14.0,14.8492424049) [29].move(1.0,0,0) [29].move(0,1.0,0)
|
||||
layer22 = new Brick.move(-13.5,-13.5,15.5563491861) [28].move(1.0,0,0) [28].move(0,1.0,0)
|
||||
layer23 = new Brick.move(-13.0,-13.0,16.2634559673) [27].move(1.0,0,0) [27].move(0,1.0,0)
|
||||
layer24 = new Brick.move(-12.5,-12.5,16.9705627485) [26].move(1.0,0,0) [26].move(0,1.0,0)
|
||||
layer25 = new Brick.move(-12.0,-12.0,17.6776695297) [25].move(1.0,0,0) [25].move(0,1.0,0)
|
||||
layer26 = new Brick.move(-11.5,-11.5,18.3847763109) [24].move(1.0,0,0) [24].move(0,1.0,0)
|
||||
layer27 = new Brick.move(-11.0,-11.0,19.091883092) [23].move(1.0,0,0) [23].move(0,1.0,0)
|
||||
layer28 = new Brick.move(-10.5,-10.5,19.7989898732) [22].move(1.0,0,0) [22].move(0,1.0,0)
|
||||
layer29 = new Brick.move(-10.0,-10.0,20.5060966544) [21].move(1.0,0,0) [21].move(0,1.0,0)
|
||||
layer30 = new Brick.move(-9.5,-9.5,21.2132034356) [20].move(1.0,0,0) [20].move(0,1.0,0)
|
||||
layer31 = new Brick.move(-9.0,-9.0,21.9203102168) [19].move(1.0,0,0) [19].move(0,1.0,0)
|
||||
layer32 = new Brick.move(-8.5,-8.5,22.627416998) [18].move(1.0,0,0) [18].move(0,1.0,0)
|
||||
layer33 = new Brick.move(-8.0,-8.0,23.3345237792) [17].move(1.0,0,0) [17].move(0,1.0,0)
|
||||
layer34 = new Brick.move(-7.5,-7.5,24.0416305603) [16].move(1.0,0,0) [16].move(0,1.0,0)
|
||||
layer35 = new Brick.move(-7.0,-7.0,24.7487373415) [15].move(1.0,0,0) [15].move(0,1.0,0)
|
||||
layer36 = new Brick.move(-6.5,-6.5,25.4558441227) [14].move(1.0,0,0) [14].move(0,1.0,0)
|
||||
layer37 = new Brick.move(-6.0,-6.0,26.1629509039) [13].move(1.0,0,0) [13].move(0,1.0,0)
|
||||
layer38 = new Brick.move(-5.5,-5.5,26.8700576851) [12].move(1.0,0,0) [12].move(0,1.0,0)
|
||||
layer39 = new Brick.move(-5.0,-5.0,27.5771644663) [11].move(1.0,0,0) [11].move(0,1.0,0)
|
||||
layer40 = new GoldBrick.move(-4.5,-4.5,28.2842712475) [10].move(1.0,0,0) [10].move(0,1.0,0)
|
||||
layer41 = new GoldBrick.move(-4.0,-4.0,28.9913780286) [9].move(1.0,0,0) [9].move(0,1.0,0)
|
||||
layer42 = new GoldBrick.move(-3.5,-3.5,29.6984848098) [8].move(1.0,0,0) [8].move(0,1.0,0)
|
||||
layer43 = new GoldBrick.move(-3.0,-3.0,30.405591591) [7].move(1.0,0,0) [7].move(0,1.0,0)
|
||||
layer44 = new GoldBrick.move(-2.5,-2.5,31.1126983722) [6].move(1.0,0,0) [6].move(0,1.0,0)
|
||||
layer45 = new GoldBrick.move(-2.0,-2.0,31.8198051534) [5].move(1.0,0,0) [5].move(0,1.0,0)
|
||||
layer46 = new GoldBrick.move(-1.5,-1.5,32.5269119346) [4].move(1.0,0,0) [4].move(0,1.0,0)
|
||||
layer47 = new GoldBrick.move(-1.0,-1.0,33.2340187158) [3].move(1.0,0,0) [3].move(0,1.0,0)
|
||||
layer48 = new GoldBrick.move(-0.5,-0.5,33.941125497) [2].move(1.0,0,0) [2].move(0,1.0,0)
|
||||
layer49 = new GoldBrick.move(0.0,0.0,34.6482322781) [1].move(1.0,0,0) [1].move(0,1.0,0)
|
||||
}
|
||||
|
||||
|
||||
PyramidKhafre {
|
||||
layer0 = new ImmobileBrick.move(-23.5,-23.5,0.0) [48].move(1.0,0,0) [48].move(0,1.0,0)
|
||||
layer1 = new Brick.move(-23.0,-23.0,0.707106781187) [47].move(1.0,0,0) [47].move(0,1.0,0)
|
||||
layer2 = new Brick.move(-22.5,-22.5,1.41421356237) [46].move(1.0,0,0) [46].move(0,1.0,0)
|
||||
layer3 = new Brick.move(-22.0,-22.0,2.12132034356) [45].move(1.0,0,0) [45].move(0,1.0,0)
|
||||
layer4 = new Brick.move(-21.5,-21.5,2.82842712475) [44].move(1.0,0,0) [44].move(0,1.0,0)
|
||||
layer5 = new Brick.move(-21.0,-21.0,3.53553390593) [43].move(1.0,0,0) [43].move(0,1.0,0)
|
||||
layer6 = new Brick.move(-20.5,-20.5,4.24264068712) [42].move(1.0,0,0) [42].move(0,1.0,0)
|
||||
layer7 = new Brick.move(-20.0,-20.0,4.94974746831) [41].move(1.0,0,0) [41].move(0,1.0,0)
|
||||
layer8 = new Brick.move(-19.5,-19.5,5.65685424949) [40].move(1.0,0,0) [40].move(0,1.0,0)
|
||||
layer9 = new Brick.move(-19.0,-19.0,6.36396103068) [39].move(1.0,0,0) [39].move(0,1.0,0)
|
||||
layer10 = new Brick.move(-18.5,-18.5,7.07106781187) [38].move(1.0,0,0) [38].move(0,1.0,0)
|
||||
layer11 = new Brick.move(-18.0,-18.0,7.77817459305) [37].move(1.0,0,0) [37].move(0,1.0,0)
|
||||
layer12 = new Brick.move(-17.5,-17.5,8.48528137424) [36].move(1.0,0,0) [36].move(0,1.0,0)
|
||||
layer13 = new Brick.move(-17.0,-17.0,9.19238815543) [35].move(1.0,0,0) [35].move(0,1.0,0)
|
||||
layer14 = new Brick.move(-16.5,-16.5,9.89949493661) [34].move(1.0,0,0) [34].move(0,1.0,0)
|
||||
layer15 = new Brick.move(-16.0,-16.0,10.6066017178) [33].move(1.0,0,0) [33].move(0,1.0,0)
|
||||
layer16 = new Brick.move(-15.5,-15.5,11.313708499) [32].move(1.0,0,0) [32].move(0,1.0,0)
|
||||
layer17 = new Brick.move(-15.0,-15.0,12.0208152802) [31].move(1.0,0,0) [31].move(0,1.0,0)
|
||||
layer18 = new Brick.move(-14.5,-14.5,12.7279220614) [30].move(1.0,0,0) [30].move(0,1.0,0)
|
||||
layer19 = new Brick.move(-14.0,-14.0,13.4350288425) [29].move(1.0,0,0) [29].move(0,1.0,0)
|
||||
layer20 = new Brick.move(-13.5,-13.5,14.1421356237) [28].move(1.0,0,0) [28].move(0,1.0,0)
|
||||
layer21 = new Brick.move(-13.0,-13.0,14.8492424049) [27].move(1.0,0,0) [27].move(0,1.0,0)
|
||||
layer22 = new Brick.move(-12.5,-12.5,15.5563491861) [26].move(1.0,0,0) [26].move(0,1.0,0)
|
||||
layer23 = new Brick.move(-12.0,-12.0,16.2634559673) [25].move(1.0,0,0) [25].move(0,1.0,0)
|
||||
layer24 = new Brick.move(-11.5,-11.5,16.9705627485) [24].move(1.0,0,0) [24].move(0,1.0,0)
|
||||
layer25 = new Brick.move(-11.0,-11.0,17.6776695297) [23].move(1.0,0,0) [23].move(0,1.0,0)
|
||||
layer26 = new Brick.move(-10.5,-10.5,18.3847763109) [22].move(1.0,0,0) [22].move(0,1.0,0)
|
||||
layer27 = new Brick.move(-10.0,-10.0,19.091883092) [21].move(1.0,0,0) [21].move(0,1.0,0)
|
||||
layer28 = new Brick.move(-9.5,-9.5,19.7989898732) [20].move(1.0,0,0) [20].move(0,1.0,0)
|
||||
layer29 = new Brick.move(-9.0,-9.0,20.5060966544) [19].move(1.0,0,0) [19].move(0,1.0,0)
|
||||
layer30 = new Brick.move(-8.5,-8.5,21.2132034356) [18].move(1.0,0,0) [18].move(0,1.0,0)
|
||||
layer31 = new Brick.move(-8.0,-8.0,21.9203102168) [17].move(1.0,0,0) [17].move(0,1.0,0)
|
||||
layer32 = new Brick.move(-7.5,-7.5,22.627416998) [16].move(1.0,0,0) [16].move(0,1.0,0)
|
||||
layer33 = new Brick.move(-7.0,-7.0,23.3345237792) [15].move(1.0,0,0) [15].move(0,1.0,0)
|
||||
layer34 = new Brick.move(-6.5,-6.5,24.0416305603) [14].move(1.0,0,0) [14].move(0,1.0,0)
|
||||
layer35 = new GoldBrick.move(-6.0,-6.0,24.7487373415) [13].move(1.0,0,0) [13].move(0,1.0,0)
|
||||
layer36 = new GoldBrick.move(-5.5,-5.5,25.4558441227) [12].move(1.0,0,0) [12].move(0,1.0,0)
|
||||
layer37 = new GoldBrick.move(-5.0,-5.0,26.1629509039) [11].move(1.0,0,0) [11].move(0,1.0,0)
|
||||
layer38 = new GoldBrick.move(-4.5,-4.5,26.8700576851) [10].move(1.0,0,0) [10].move(0,1.0,0)
|
||||
layer39 = new GoldBrick.move(-4.0,-4.0,27.5771644663) [9].move(1.0,0,0) [9].move(0,1.0,0)
|
||||
layer40 = new GoldBrick.move(-3.5,-3.5,28.2842712475) [8].move(1.0,0,0) [8].move(0,1.0,0)
|
||||
layer41 = new GoldBrick.move(-3.0,-3.0,28.9913780286) [7].move(1.0,0,0) [7].move(0,1.0,0)
|
||||
layer42 = new GoldBrick.move(-2.5,-2.5,29.6984848098) [6].move(1.0,0,0) [6].move(0,1.0,0)
|
||||
layer43 = new GoldBrick.move(-2.0,-2.0,30.405591591) [5].move(1.0,0,0) [5].move(0,1.0,0)
|
||||
layer44 = new GoldBrick.move(-1.5,-1.5,31.1126983722) [4].move(1.0,0,0) [4].move(0,1.0,0)
|
||||
layer45 = new GoldBrick.move(-1.0,-1.0,31.8198051534) [3].move(1.0,0,0) [3].move(0,1.0,0)
|
||||
layer46 = new GoldBrick.move(-0.5,-0.5,32.5269119346) [2].move(1.0,0,0) [2].move(0,1.0,0)
|
||||
layer47 = new GoldBrick.move(0.0,0.0,33.2340187158) [1].move(1.0,0,0) [1].move(0,1.0,0)
|
||||
}
|
||||
|
||||
|
||||
PyramidMenkaure {
|
||||
layer0 = new ImmobileBrick.move(-9.0,-9.0,0.0) [19].move(1.0,0,0) [19].move(0,1.0,0)
|
||||
layer1 = new Brick.move(-8.5,-8.5,0.707106781187) [18].move(1.0,0,0) [18].move(0,1.0,0)
|
||||
layer2 = new Brick.move(-8.0,-8.0,1.41421356237) [17].move(1.0,0,0) [17].move(0,1.0,0)
|
||||
layer3 = new Brick.move(-7.5,-7.5,2.12132034356) [16].move(1.0,0,0) [16].move(0,1.0,0)
|
||||
layer4 = new Brick.move(-7.0,-7.0,2.82842712475) [15].move(1.0,0,0) [15].move(0,1.0,0)
|
||||
layer5 = new Brick.move(-6.5,-6.5,3.53553390593) [14].move(1.0,0,0) [14].move(0,1.0,0)
|
||||
layer6 = new Brick.move(-6.0,-6.0,4.24264068712) [13].move(1.0,0,0) [13].move(0,1.0,0)
|
||||
layer7 = new Brick.move(-5.5,-5.5,4.94974746831) [12].move(1.0,0,0) [12].move(0,1.0,0)
|
||||
layer8 = new Brick.move(-5.0,-5.0,5.65685424949) [11].move(1.0,0,0) [11].move(0,1.0,0)
|
||||
layer9 = new Brick.move(-4.5,-4.5,6.36396103068) [10].move(1.0,0,0) [10].move(0,1.0,0)
|
||||
layer10 = new Brick.move(-4.0,-4.0,7.07106781187) [9].move(1.0,0,0) [9].move(0,1.0,0)
|
||||
layer11 = new Brick.move(-3.5,-3.5,7.77817459305) [8].move(1.0,0,0) [8].move(0,1.0,0)
|
||||
layer12 = new Brick.move(-3.0,-3.0,8.48528137424) [7].move(1.0,0,0) [7].move(0,1.0,0)
|
||||
layer13 = new Brick.move(-2.5,-2.5,9.19238815543) [6].move(1.0,0,0) [6].move(0,1.0,0)
|
||||
layer14 = new Brick.move(-2.0,-2.0,9.89949493661) [5].move(1.0,0,0) [5].move(0,1.0,0)
|
||||
layer15 = new Brick.move(-1.5,-1.5,10.6066017178) [4].move(1.0,0,0) [4].move(0,1.0,0)
|
||||
layer16 = new Brick.move(-1.0,-1.0,11.313708499) [3].move(1.0,0,0) [3].move(0,1.0,0)
|
||||
layer17 = new Brick.move(-0.5,-0.5,12.0208152802) [2].move(1.0,0,0) [2].move(0,1.0,0)
|
||||
layer18 = new Brick.move(0.0,0.0,12.7279220614) [1].move(1.0,0,0) [1].move(0,1.0,0)
|
||||
}
|
||||
|
||||
PyramidQueens1 {
|
||||
layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0)
|
||||
layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0)
|
||||
layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0)
|
||||
layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0)
|
||||
layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0)
|
||||
layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0)
|
||||
}
|
||||
|
||||
PyramidQueens2 {
|
||||
layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0)
|
||||
layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0)
|
||||
layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0)
|
||||
layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0)
|
||||
layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0)
|
||||
layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0)
|
||||
}
|
||||
|
||||
PyramidQueens3 {
|
||||
layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0)
|
||||
layer1 = new Brick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0)
|
||||
layer2 = new Brick.move(-2.5,-2.5,1.41421356237) [6].move(1.0,0,0) [6].move(0,1.0,0)
|
||||
layer3 = new Brick.move(-2.0,-2.0,2.12132034356) [5].move(1.0,0,0) [5].move(0,1.0,0)
|
||||
layer4 = new Brick.move(-1.5,-1.5,2.82842712475) [4].move(1.0,0,0) [4].move(0,1.0,0)
|
||||
layer5 = new Brick.move(-1.0,-1.0,3.53553390593) [3].move(1.0,0,0) [3].move(0,1.0,0)
|
||||
layer6 = new Brick.move(-0.5,-0.5,4.24264068712) [2].move(1.0,0,0) [2].move(0,1.0,0)
|
||||
layer7 = new Brick.move(0.0,0.0,4.94974746831) [1].move(1.0,0,0) [1].move(0,1.0,0)
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
# "ImmobileBrick"s are identical to "Brick"s,
|
||||
# except that they have a different atom type.
|
||||
# We can define groups based on atom type
|
||||
# and apply fixes to them.
|
||||
|
||||
ImmobileBrick {
|
||||
|
||||
# atomID molID atomType charge x y z
|
||||
write("Data Atoms") {
|
||||
$atom $mol @atom 0.0 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom 1.0
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6)
|
||||
#
|
||||
# i j eps sig
|
||||
pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
group gImmobile type @atom
|
||||
# (Atoms of this type belong to the "gImmobile" group)
|
||||
}
|
||||
|
||||
write_once("In Init") {
|
||||
atom_style full
|
||||
units lj
|
||||
pair_style hybrid lj/cut 1.0
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
GoldBrick {
|
||||
|
||||
# atomID molID atomType charge x y z
|
||||
write("Data Atoms") {
|
||||
$atom $mol @atom 0.0 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom 1.0
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6)
|
||||
#
|
||||
# i j eps sig
|
||||
pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
group gMobile type @atom
|
||||
# (Atoms of this type belong to the "gMobile" group)
|
||||
}
|
||||
|
||||
write_once("In Init") {
|
||||
atom_style full
|
||||
units lj
|
||||
pair_style lj/cut 1.0
|
||||
}
|
||||
}
|
||||
|
||||
@ -0,0 +1,80 @@
|
||||
# Description.
|
||||
# This is a simulation of pyramid-like objects made of particles stacked
|
||||
# and arranged like cannon-balls, or fruit-stands. Ordinarilly, the stack
|
||||
# does not collapse because the particles at the ground layer are immobilized.
|
||||
# However given an initial perterbation the pyramids collapse in an avalanche.
|
||||
# (This can happen, for example when you do not minimize the system beforehand.)
|
||||
# The particles roll down the pyramid and bounce off the "ground". The bouncing
|
||||
# is due to a repulsive external force which is added artificially.
|
||||
# (See the "run.in" file.) The simulation looks weird without something
|
||||
# to bounce off of. So I added a graphene surface at the bottom as scenery.
|
||||
# The ground does not serve any purpose except to look pretty.
|
||||
#
|
||||
# (Because there is no damping, I suspect that the distribution of heights of
|
||||
# the particles in a small area should approach the Boltzmann distribution,
|
||||
# if you run the simulation long enough.)
|
||||
|
||||
|
||||
# ----------------- Pyramids: -----------------
|
||||
|
||||
import "pyramids.lt"
|
||||
|
||||
# Move the pyramids into their locations in Giza (approximate)
|
||||
|
||||
pyramidKhufu = new PyramidKhufu.move(210, 215, 1)
|
||||
pyramidKhafre = new PyramidKhafre.move(150, 150, 1)
|
||||
pyramidMenkaure = new PyramidMenkaure.move(105, 082, 1)
|
||||
PyramidQueens1 = new PyramidQueens1.move(089, 059, 1)
|
||||
PyramidQueens2 = new PyramidQueens2.move(100, 059, 1)
|
||||
PyramidQueens3 = new PyramidQueens3.move(111, 059, 1)
|
||||
|
||||
|
||||
# --------------- Scenery: --------------------
|
||||
|
||||
import "graphene_wall.lt"
|
||||
|
||||
graphene_wall = new GrapheneWall
|
||||
|
||||
write_once("In Settings") {
|
||||
# Turn off all interactions with the graphene atoms by setting epsilon to 0.
|
||||
# (We will use a different repulsive barrier to represent the ground instead.)
|
||||
# These atoms are just "for show". epsilon sigma
|
||||
pair_coeff @atom:Graphene/C @atom:Graphene/C lj/cut 0.00000 3.407
|
||||
|
||||
# Optional: Add the graphene atoms to the "gImmobile" group. Later freeze them
|
||||
group gImmobile type @atom:Graphene/C
|
||||
}
|
||||
|
||||
# Unfortunately, the ground still looks kind of ugly because moltemplate does
|
||||
# not yet know how to automatically connect nearby carbon atoms with C-C bonds
|
||||
# (based on distance). (As of 2013-4-29, moltemplate is not good at
|
||||
# generating crystalline objects containing explicit bonds.)
|
||||
# If you want bonds between atoms, use VMD's "carbon-nanotube-builder plugin"
|
||||
# (which creates data files with bonds) and then merge the two data files
|
||||
# manually later. (This is not done here.)
|
||||
|
||||
|
||||
# -------- override earlier settings ----------
|
||||
|
||||
write_once("In Init") {
|
||||
# Override any earlier style settings
|
||||
atom_style full
|
||||
units lj
|
||||
pair_style hybrid lj/cut 1.0
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
# ------------ boundary conditions ------------
|
||||
|
||||
write_once("Data Boundary") {
|
||||
-1.842033 398.493813 xlo xhi
|
||||
-0.708994 399.167013 ylo yhi
|
||||
0.0 400.0 zlo zhi
|
||||
}
|
||||
# ---------------------------------------------
|
||||
|
||||
@ -0,0 +1,64 @@
|
||||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
boundary p p f
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
|
||||
timestep 0.0025
|
||||
dump 1 all custom 200 traj_nvt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
thermo_style custom step temp pe etotal
|
||||
thermo 100 # time interval for printing out "thermo" data
|
||||
|
||||
# ---- Set up the physical environment ----
|
||||
|
||||
# Add gravity:
|
||||
fix fxGrav gMobile gravity 0.05 vector 0 0 -1
|
||||
|
||||
# Create a "ground" surface.
|
||||
# This is a repulsive "wall" which particles can bounce off of:
|
||||
|
||||
fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0
|
||||
|
||||
|
||||
# ---- Evolve the system: ----
|
||||
|
||||
# Evolve the (mobile) atoms using ordinary Newton's laws (NVE)
|
||||
|
||||
fix fxNVE gMobile nve
|
||||
|
||||
|
||||
# IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE:
|
||||
#fix fxLan gMobile langevin 0.001 0.001 10000.0 48279
|
||||
# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve"
|
||||
# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
|
||||
# This was not tested.
|
||||
|
||||
# For efficient simulation in parallel, try using "fix balance":
|
||||
# (This will adjust the spatial decomposition as the distribution of
|
||||
# particles changes over time.)
|
||||
|
||||
fix fxBalance gMobile balance 1000 xy 20 1.3
|
||||
|
||||
# Optional: Improve efficiency by omitting the calcuation of interactions
|
||||
# between immobile atoms:
|
||||
|
||||
neigh_modify exclude group gImmobile gImmobile
|
||||
|
||||
|
||||
restart 50000 restart_nvt
|
||||
|
||||
run 200000
|
||||
|
||||
write_data system_after_nvt.data
|
||||
|
||||
Reference in New Issue
Block a user