[ViewVC] Contents 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.
#
# The thermalizer command takes the FCC.md file and resamples the velocities
# from a Maxwell-Boltzmann distribution set to 100K:
#
../../bin/simpleBuilder -o FCC.md --nx=5 --ny=5 --nz=5 --density=1.0 one_component.md
../../bin/thermalizer -o FCC-100K.md -t 100 FCC.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
../../bin/thermalizer -o random_FCC-100K.md -t 100 random_FCC.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
../../bin/thermalizer -o gold_sphere-500K.md -t 500.0 gold_sphere.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
../../bin/thermalizer -o Au_Ag_alloy-600K.md -t 600 Au_Ag_alloy.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
../../bin/thermalizer -o Au-core-Ag-shell-800K.md -t 800.0 Au-core-Ag-shell.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
../../bin/thermalizer -o Ag-core-Au-shell-800K.md -t 800.0 Ag-core-Au-shell.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
../../bin/thermalizer -o vacancy_interface-800K.md -t 800 vacancy_interface.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
../../bin/thermalizer -o vacancy_alloy-900K.md -t 900 vacancy_alloy.md
Revision:	3059
Committed:	Fri Oct 20 14:59:05 2006 UTC (17 years, 11 months ago) by gezelter
File size:	5657 byte(s)
Log Message:	more openbabel updates, also changing velocitizer to thermalizer to avoid a filename collision on case-insensitve file systems
#	Content
1	#!/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	# 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	# The thermalizer command takes the FCC.md file and resamples the velocities
23	# from a Maxwell-Boltzmann distribution set to 100K:
24	#
25	../../bin/simpleBuilder -o FCC.md --nx=5 --ny=5 --nz=5 --density=1.0 one_component.md
26	../../bin/thermalizer -o FCC-100K.md -t 100 FCC.md
27	#
28	# Example 2:
29	# Builds an FCC lattice from the <MetaData> block in three_component.md
30	# uses 4 unit cells in each direction, a density of 1.0 g / cm^3, and
31	# molFractions of 0.4, 0.4, and 0.2 for the three components. Places
32	# the output (which can be used to start an OOPSE job) in random_FCC.md
33	#
34	# Note that builders will rewrite the number of molecules in each component
35	# to match the number of lattice sites.
36	#
37	../../bin/randomBuilder -o random_FCC.md --nx=4 --ny=4 --nz=4 --density=1.0 --molFraction=0.4 --molFraction=0.4 three_component.md
38	../../bin/thermalizer -o random_FCC-100K.md -t 100 random_FCC.md
39	#
40	# Example 3:
41	# Builds a spherical nanoparticle (FCC) from the <MetaData> block in gold.md
42	# using a particle radius of 30 Angstroms, and a lattice constant of 4.09
43	# angstroms. Places the output (which can be used to start an OOPSE job) in
44	# gold_sphere.md
45	#
46	# Note that builders will rewrite the number of molecules in each component
47	# to match the number of lattice sites.
48	#
49	../../bin/nanoparticleBuilder -o gold_sphere.md --radius=30.0 --latticeConstant=4.09 gold.md
50	../../bin/thermalizer -o gold_sphere-500K.md -t 500.0 gold_sphere.md
51	#
52	# Example 4:
53	# Builds a random alloy spherical nanoparticle (FCC) from the <MetaData>
54	# block in bimetallic.md using a particle radius of 30 Angstroms, a
55	# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4.
56	# Places the output (which can be used to start an OOPSE job) in
57	# Au_Ag_alloy.md
58	#
59	# Note that builders will rewrite the number of molecules in each component
60	# to match the number of lattice sites.
61	#
62	../../bin/nanoparticleBuilder -o Au_Ag_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 bimetallic.md
63	../../bin/thermalizer -o Au_Ag_alloy-600K.md -t 600 Au_Ag_alloy.md
64	#
65	# Example 5:
66	# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData>
67	# block in bimetallic.md using a particle radius of 25 Angstroms, a
68	# lattice constant of 4.09 angstroms, and a core radius for the gold atoms
69	# of 12.5 angstroms. Places the output (which can be used to start an
70	# OOPSE job) in Au(core)-Ag(shell).md
71	#
72	# Note that builders will rewrite the number of molecules in each component
73	# to match the number of lattice sites.
74	#
75	../../bin/nanoparticleBuilder -o Au-core-Ag-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=12.5 bimetallic.md
76	../../bin/thermalizer -o Au-core-Ag-shell-800K.md -t 800.0 Au-core-Ag-shell.md
77	#
78	# Example 6:
79	# Reverses example 5 by building a Ag(core)-Au(shell) spherical nanoparticle.
80	# Uses the same <MetaData> block from bimetallic.md,
81	# a particle radius of 25 Angstroms, a lattice constant of 4.09 angstroms,
82	# and a core radius for the silver atoms of 12.5 angstroms.
83	# Places the output (which can be used to start an OOPSE job) in
84	# Ag(core)-Au(shell).md
85	#
86	# Note that the last radius in Example 5 was taken as the particle radius,
87	# but since the components are reversed in this example, both are specified:
88	#
89	#
90	../../bin/nanoparticleBuilder -o Ag-core-Au-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=30.0,12.5 bimetallic.md
91	../../bin/thermalizer -o Ag-core-Au-shell-800K.md -t 800.0 Ag-core-Au-shell.md
92	#
93	# Example 7:
94	# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData>
95	# block in bimetallic.md using a particle radius of 25 Angstroms, a
96	# lattice constant of 4.09 angstroms, and a core radius for the gold atoms
97	# of 12.5 angstroms. Places the output (which can be used to start an
98	# OOPSE job) in Au(core)-Ag(shell).md
99	#
100	# This example also introduces 70% vacancies in a 6 angstrom radial band
101	# around the bimetallic interface:
102	#
103	../../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
104	../../bin/thermalizer -o vacancy_interface-800K.md -t 800 vacancy_interface.md
105	#
106	# Example 8:
107	# Builds a random alloy spherical nanoparticle with 30% vacancies using the
108	# <MetaData> block in bimetallic.md, a particle radius of 30 Angstroms, a
109	# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4.
110	# Places the output (which can be used to start an OOPSE job) in
111	# vacancy_alloy.md
112	#
113	../../bin/nanoparticleBuilder -o vacancy_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 --vacancyPercent=80 bimetallic.md
114	../../bin/thermalizer -o vacancy_alloy-900K.md -t 900 vacancy_alloy.md