[ViewVC] Annotation of: group/trunk/OOPSE-4/samples/builders/runMe

#!/bin/sh
#
# This is a collection of sample commands that can be used to build
# OOPSE 4 start files.  In OOPSE 4, the start files have a <MetaData>
# block to give information about the kind of simulation being performed.
# The start files also contain at least one <Snapshot> block which contains
# information about the instantaneous configuration.  
#
# One of the difficult tasks in using any simulation program is figuring
# out how to format the start file correctly.  OOPSE includes a set of
# "builder" programs to make that process a bit less painful.
#
# Example 1:
# Builds an FCC lattice from the <MetaData> block in one_component.md
# Uses 5 unit cells in each direction, a density of 1.0 g / cm^3, and
# places the output (which can be used to start an OOPSE job) in 
# FCC.md
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
../../bin/simpleBuilder -o FCC.md --nx=5 --ny=5 --nz=5 --density=1.0 one_component.md
#
# Example 2:
# Builds an FCC lattice from the <MetaData> block in three_component.md
# uses 4 unit cells in each direction, a density of 1.0 g / cm^3, and
# molFractions of 0.4, 0.4, and 0.2 for the three components.  Places
# the output (which can be used to start an OOPSE job) in random_FCC.md
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
../../bin/randomBuilder -o random_FCC.md --nx=4 --ny=4 --nz=4 --density=1.0 --molFraction=0.4 --molFraction=0.4 three_component.md
#
# Example 3:
# Builds a spherical nanoparticle (FCC) from the <MetaData> block in gold.md
# using a particle radius of 30 Angstroms, and a lattice constant of 4.09
# angstroms. Places the output (which can be used to start an OOPSE job) in 
# gold_sphere.md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
../../bin/nanoparticleBuilder -o gold_sphere.md --radius=30.0 --latticeConstant=4.09 gold.md
#
# Example 4:
# Builds a random alloy spherical nanoparticle (FCC) from the <MetaData> 
# block in bimetallic.md using a particle radius of 30 Angstroms, a 
# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4.
# Places the output (which can be used to start an OOPSE job) in 
# Au_Ag_alloy.md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
../../bin/nanoparticleBuilder -o Au_Ag_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 bimetallic.md
#
# Example 5:
# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData> 
# block in bimetallic.md using a particle radius of 25 Angstroms, a 
# lattice constant of 4.09 angstroms, and a core radius for the gold atoms 
# of 12.5 angstroms. Places the output (which can be used to start an 
# OOPSE job) in Au(core)-Ag(shell).md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
../../bin/nanoparticleBuilder -o Au\(core\)-Ag\(shell\).md --radius=30.0 --latticeConstant=4.09 --shellRadius=12.5 bimetallic.md
#
# Example 6:
# Reverses example 5 by building a Ag(core)-Au(shell) spherical nanoparticle.
# Uses the same <MetaData> block from bimetallic.md, 
# a particle radius of 25 Angstroms, a lattice constant of 4.09 angstroms, 
# and a core radius for the silver atoms of 12.5 angstroms.  
# Places the output (which can be used to start an OOPSE job) in 
# Ag(core)-Au(shell).md 
#
# Note that the last radius in Example 5 was taken as the particle radius,
# but since the components are reversed in this example, both are specified:
# 
#
../../bin/nanoparticleBuilder -o Ag\(core\)-Au\(shell\).md --radius=30.0 --latticeConstant=4.09 --shellRadius=30.0,12.5 bimetallic.md
#
# Example 7:
# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData> 
# block in bimetallic.md using a particle radius of 25 Angstroms, a 
# lattice constant of 4.09 angstroms, and a core radius for the gold atoms 
# of 12.5 angstroms. Places the output (which can be used to start an 
# OOPSE job) in Au(core)-Ag(shell).md 
#
# This example also introduces 70% vacancies in a 6 angstrom radial band
# around the bimetallic interface:
#
../../bin/nanoparticleBuilder -o vacancy_interface.md --radius=20.0 --latticeConstant=4.09 --shellRadius=12.5 --vacancyPercent=70 --vacancyInnerRadius=9.5 --vacancyOuterRadius=15.5 bimetallic.md
#
# Example 8:
# Builds a random alloy spherical nanoparticle with 30% vacancies using the
# <MetaData> block in bimetallic.md, a particle radius of 30 Angstroms, a 
# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4.
# Places the output (which can be used to start an OOPSE job) in 
# vacancy_alloy.md
#
../../bin/nanoparticleBuilder -o vacancy_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 --vacancyPercent=80 bimetallic.md
Revision:	3052
Committed:	Wed Oct 18 19:34:38 2006 UTC (17 years, 11 months ago) by gezelter
File size:	4977 byte(s)
Log Message:	Adding samples for builders
#	User	Rev	Content
1	gezelter	3040	#!/bin/sh
2			#
3			# This is a collection of sample commands that can be used to build
4			# OOPSE 4 start files. In OOPSE 4, the start files have a <MetaData>
5			# block to give information about the kind of simulation being performed.
6			# The start files also contain at least one <Snapshot> block which contains
7			# information about the instantaneous configuration.
8			#
9			# One of the difficult tasks in using any simulation program is figuring
10			# out how to format the start file correctly. OOPSE includes a set of
11			# "builder" programs to make that process a bit less painful.
12			#
13			# Example 1:
14	gezelter	3041	# Builds an FCC lattice from the <MetaData> block in one_component.md
15			# Uses 5 unit cells in each direction, a density of 1.0 g / cm^3, and
16			# places the output (which can be used to start an OOPSE job) in
17			# FCC.md
18			#
19			# Note that builders will rewrite the number of molecules in each component
20			# to match the number of lattice sites.
21			#
22			../../bin/simpleBuilder -o FCC.md --nx=5 --ny=5 --nz=5 --density=1.0 one_component.md
23			#
24			# Example 2:
25	gezelter	3040	# Builds an FCC lattice from the <MetaData> block in three_component.md
26			# uses 4 unit cells in each direction, a density of 1.0 g / cm^3, and
27			# molFractions of 0.4, 0.4, and 0.2 for the three components. Places
28			# the output (which can be used to start an OOPSE job) in random_FCC.md
29			#
30			# Note that builders will rewrite the number of molecules in each component
31			# to match the number of lattice sites.
32			#
33			../../bin/randomBuilder -o random_FCC.md --nx=4 --ny=4 --nz=4 --density=1.0 --molFraction=0.4 --molFraction=0.4 three_component.md
34	gezelter	3052	#
35			# Example 3:
36			# Builds a spherical nanoparticle (FCC) from the <MetaData> block in gold.md
37			# using a particle radius of 30 Angstroms, and a lattice constant of 4.09
38			# angstroms. Places the output (which can be used to start an OOPSE job) in
39			# gold_sphere.md
40			#
41			# Note that builders will rewrite the number of molecules in each component
42			# to match the number of lattice sites.
43			#
44			../../bin/nanoparticleBuilder -o gold_sphere.md --radius=30.0 --latticeConstant=4.09 gold.md
45			#
46			# Example 4:
47			# Builds a random alloy spherical nanoparticle (FCC) from the <MetaData>
48			# block in bimetallic.md using a particle radius of 30 Angstroms, a
49			# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4.
50			# Places the output (which can be used to start an OOPSE job) in
51			# Au_Ag_alloy.md
52			#
53			# Note that builders will rewrite the number of molecules in each component
54			# to match the number of lattice sites.
55			#
56			../../bin/nanoparticleBuilder -o Au_Ag_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 bimetallic.md
57			#
58			# Example 5:
59			# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData>
60			# block in bimetallic.md using a particle radius of 25 Angstroms, a
61			# lattice constant of 4.09 angstroms, and a core radius for the gold atoms
62			# of 12.5 angstroms. Places the output (which can be used to start an
63			# OOPSE job) in Au(core)-Ag(shell).md
64			#
65			# Note that builders will rewrite the number of molecules in each component
66			# to match the number of lattice sites.
67			#
68			../../bin/nanoparticleBuilder -o Au\(core\)-Ag\(shell\).md --radius=30.0 --latticeConstant=4.09 --shellRadius=12.5 bimetallic.md
69			#
70			# Example 6:
71			# Reverses example 5 by building a Ag(core)-Au(shell) spherical nanoparticle.
72			# Uses the same <MetaData> block from bimetallic.md,
73			# a particle radius of 25 Angstroms, a lattice constant of 4.09 angstroms,
74			# and a core radius for the silver atoms of 12.5 angstroms.
75			# Places the output (which can be used to start an OOPSE job) in
76			# Ag(core)-Au(shell).md
77			#
78			# Note that the last radius in Example 5 was taken as the particle radius,
79			# but since the components are reversed in this example, both are specified:
80			#
81			#
82			../../bin/nanoparticleBuilder -o Ag\(core\)-Au\(shell\).md --radius=30.0 --latticeConstant=4.09 --shellRadius=30.0,12.5 bimetallic.md
83			#
84			# Example 7:
85			# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData>
86			# block in bimetallic.md using a particle radius of 25 Angstroms, a
87			# lattice constant of 4.09 angstroms, and a core radius for the gold atoms
88			# of 12.5 angstroms. Places the output (which can be used to start an
89			# OOPSE job) in Au(core)-Ag(shell).md
90			#
91			# This example also introduces 70% vacancies in a 6 angstrom radial band
92			# around the bimetallic interface:
93			#
94			../../bin/nanoparticleBuilder -o vacancy_interface.md --radius=20.0 --latticeConstant=4.09 --shellRadius=12.5 --vacancyPercent=70 --vacancyInnerRadius=9.5 --vacancyOuterRadius=15.5 bimetallic.md
95			#
96			# Example 8:
97			# Builds a random alloy spherical nanoparticle with 30% vacancies using the
98			# <MetaData> block in bimetallic.md, a particle radius of 30 Angstroms, a
99			# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4.
100			# Places the output (which can be used to start an OOPSE job) in
101			# vacancy_alloy.md
102			#
103			../../bin/nanoparticleBuilder -o vacancy_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 --vacancyPercent=80 bimetallic.md