samples/builders/runMe.in

#!/bin/sh
OPENMD_HOME=@CMAKE_INSTALL_PREFIX@
# This is a collection of sample commands that can be used to build
# OpenMD start files.  In OpenMD, 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.  OpenMD 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 OpenMD 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:
#
${OPENMD_HOME}/bin/simpleBuilder -o FCC.md --nx=5 --ny=5 --nz=5 --density=1.0 one_component.md
${OPENMD_HOME}/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 OpenMD job) in random_FCC.md
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
${OPENMD_HOME}/bin/randomBuilder -o random_FCC.md --nx=4 --ny=4 --nz=4 --density=1.0 --molFraction=0.4 --molFraction=0.4 three_component.md
${OPENMD_HOME}/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 OpenMD job) in 
# gold_sphere.md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
${OPENMD_HOME}/bin/nanoparticleBuilder -o gold_sphere.md --radius=30.0 --latticeConstant=4.09 gold.md
${OPENMD_HOME}/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 OpenMD 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.
#
${OPENMD_HOME}/bin/nanoparticleBuilder -o Au_Ag_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 bimetallic.md
${OPENMD_HOME}/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 
# OpenMD 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.
#
${OPENMD_HOME}/bin/nanoparticleBuilder -o Au-core-Ag-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=12.5 bimetallic.md
${OPENMD_HOME}/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 OpenMD 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:
# 
#
${OPENMD_HOME}/bin/nanoparticleBuilder -o Ag-core-Au-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=30.0,12.5 bimetallic.md
${OPENMD_HOME}/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 
# OpenMD job) in Au(core)-Ag(shell).md 
#
# This example also introduces 70% vacancies in a 6 angstrom radial band
# around the bimetallic interface:
#
${OPENMD_HOME}/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
${OPENMD_HOME}/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 OpenMD job) in 
# vacancy_alloy.md
#
${OPENMD_HOME}/bin/nanoparticleBuilder -o vacancy_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 --vacancyPercent=80 bimetallic.md
${OPENMD_HOME}/bin/thermalizer -o vacancy_alloy-900K.md -t 900 vacancy_alloy.md
#
#Example 9:
# Builds a spherically-capped nanorod (FCC) from the <MetaData> block in gold.md
# using a nanorod radius of 20 Angstroms, a length of 50 Angstroms and a lattice constant of 4.08
# angstroms. Places the output (which can be used to start an OpenMD job) in 
# gold_fccrod.md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
${OPENMD_HOME}/bin/nanorodBuilder -o gold_fccrod.md --radius=20.0 --length=50.0 --latticeConstant=4.08 gold.md
#
#Example 10:
# Builds a pentagonal nanorod from the <MetaData> block in gold.md
# using a nanorod radius of 15 Angstroms, a length of 64 Angstroms and a lattice constant of 4.08
# angstroms. Places the output (which can be used to start an OpenMD job) in 
# gold_pentrod.md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
${OPENMD_HOME}/bin/nanorod_pentBuilder -o gold_pentrod.md --radius=15.0 --length=64.0 --latticeConstant=4.08 gold.md
#
#Example 11:
# Builds a Mackay icosahedral nanoparticle from the <MetaData> block in gold.md
# using a 8 shells, and a lattice constant of 4.08 angstroms.
# Places the output (which can be used to start an OpenMD job) in 
# gold_ico.md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
${OPENMD_HOME}/bin/icosahedralBuilder -o gold_ico.md --shells=8 --latticeConstant=4.08 gold.md
${OPENMD_HOME}/bin/thermalizer -o gold_ico_300K.md -t 300 gold_ico.md
Revision:	1861
Committed:	Tue Apr 9 19:45:54 2013 UTC (12 years ago) by gezelter
File size:	7399 byte(s)
Log Message:	Added a Harmonic Torsion Type, fixed some bugs in RNEMD and waterReplacer.
#	User	Rev	Content
1	gezelter	1066	#!/bin/sh
2	gezelter	1805	OPENMD_HOME=@CMAKE_INSTALL_PREFIX@
3	gezelter	1066	# This is a collection of sample commands that can be used to build
4	gezelter	1390	# OpenMD start files. In OpenMD, the start files have a <MetaData>
5	gezelter	1066	# 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	gezelter	1390	# out how to format the start file correctly. OpenMD includes a set of
11	gezelter	1066	# "builder" programs to make that process a bit less painful.
12			#
13			# Example 1:
14	gezelter	1067	# 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	gezelter	1390	# places the output (which can be used to start an OpenMD job) in
17	gezelter	1067	# 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	gezelter	1083	# The thermalizer command takes the FCC.md file and resamples the velocities
23	gezelter	1079	# from a Maxwell-Boltzmann distribution set to 100K:
24			#
25	gezelter	1805	${OPENMD_HOME}/bin/simpleBuilder -o FCC.md --nx=5 --ny=5 --nz=5 --density=1.0 one_component.md
26			${OPENMD_HOME}/bin/thermalizer -o FCC-100K.md -t 100 FCC.md
27	gezelter	1067	#
28			# Example 2:
29	gezelter	1066	# 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	gezelter	1390	# the output (which can be used to start an OpenMD job) in random_FCC.md
33	gezelter	1066	#
34			# Note that builders will rewrite the number of molecules in each component
35			# to match the number of lattice sites.
36			#
37	gezelter	1805	${OPENMD_HOME}/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			${OPENMD_HOME}/bin/thermalizer -o random_FCC-100K.md -t 100 random_FCC.md
39	gezelter	1076	#
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	gezelter	1390	# angstroms. Places the output (which can be used to start an OpenMD job) in
44	gezelter	1076	# 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	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o gold_sphere.md --radius=30.0 --latticeConstant=4.09 gold.md
50			${OPENMD_HOME}/bin/thermalizer -o gold_sphere-500K.md -t 500.0 gold_sphere.md
51	gezelter	1076	#
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	gezelter	1390	# Places the output (which can be used to start an OpenMD job) in
57	gezelter	1076	# 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	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o Au_Ag_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 bimetallic.md
63			${OPENMD_HOME}/bin/thermalizer -o Au_Ag_alloy-600K.md -t 600 Au_Ag_alloy.md
64	gezelter	1076	#
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	gezelter	1390	# OpenMD job) in Au(core)-Ag(shell).md
71	gezelter	1076	#
72			# Note that builders will rewrite the number of molecules in each component
73			# to match the number of lattice sites.
74			#
75	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o Au-core-Ag-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=12.5 bimetallic.md
76			${OPENMD_HOME}/bin/thermalizer -o Au-core-Ag-shell-800K.md -t 800.0 Au-core-Ag-shell.md
77	gezelter	1076	#
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	gezelter	1390	# Places the output (which can be used to start an OpenMD job) in
84	gezelter	1076	# 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	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o Ag-core-Au-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=30.0,12.5 bimetallic.md
91			${OPENMD_HOME}/bin/thermalizer -o Ag-core-Au-shell-800K.md -t 800.0 Ag-core-Au-shell.md
92	gezelter	1076	#
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	gezelter	1390	# OpenMD job) in Au(core)-Ag(shell).md
99	gezelter	1076	#
100			# This example also introduces 70% vacancies in a 6 angstrom radial band
101			# around the bimetallic interface:
102			#
103	gezelter	1805	${OPENMD_HOME}/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			${OPENMD_HOME}/bin/thermalizer -o vacancy_interface-800K.md -t 800 vacancy_interface.md
105	gezelter	1076	#
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	gezelter	1390	# Places the output (which can be used to start an OpenMD job) in
111	gezelter	1076	# vacancy_alloy.md
112			#
113	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o vacancy_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 --vacancyPercent=80 bimetallic.md
114			${OPENMD_HOME}/bin/thermalizer -o vacancy_alloy-900K.md -t 900 vacancy_alloy.md
115	gezelter	1782	#
116			#Example 9:
117			# Builds a spherically-capped nanorod (FCC) from the <MetaData> block in gold.md
118			# using a nanorod radius of 20 Angstroms, a length of 50 Angstroms and a lattice constant of 4.08
119			# angstroms. Places the output (which can be used to start an OpenMD job) in
120			# gold_fccrod.md
121			#
122			# Note that builders will rewrite the number of molecules in each component
123			# to match the number of lattice sites.
124			#
125	gezelter	1805	${OPENMD_HOME}/bin/nanorodBuilder -o gold_fccrod.md --radius=20.0 --length=50.0 --latticeConstant=4.08 gold.md
126	gezelter	1782	#
127			#Example 10:
128			# Builds a pentagonal nanorod from the <MetaData> block in gold.md
129			# using a nanorod radius of 15 Angstroms, a length of 64 Angstroms and a lattice constant of 4.08
130			# angstroms. Places the output (which can be used to start an OpenMD job) in
131			# gold_pentrod.md
132			#
133			# Note that builders will rewrite the number of molecules in each component
134			# to match the number of lattice sites.
135			#
136	gezelter	1805	${OPENMD_HOME}/bin/nanorod_pentBuilder -o gold_pentrod.md --radius=15.0 --length=64.0 --latticeConstant=4.08 gold.md
137	gezelter	1861	#
138			#Example 11:
139			# Builds a Mackay icosahedral nanoparticle from the <MetaData> block in gold.md
140			# using a 8 shells, and a lattice constant of 4.08 angstroms.
141			# Places the output (which can be used to start an OpenMD job) in
142			# gold_ico.md
143			#
144			# Note that builders will rewrite the number of molecules in each component
145			# to match the number of lattice sites.
146			#
147			${OPENMD_HOME}/bin/icosahedralBuilder -o gold_ico.md --shells=8 --latticeConstant=4.08 gold.md
148			${OPENMD_HOME}/bin/thermalizer -o gold_ico_300K.md -t 300 gold_ico.md