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
${OPENMD_HOME}/bin/Dump2XYZ -i FCC-100K.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
${OPENMD_HOME}/bin/Dump2XYZ -i random_FCC-100K.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
${OPENMD_HOME}/bin/Dump2XYZ -i gold_sphere-500K.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
${OPENMD_HOME}/bin/Dump2XYZ -i Au_Ag_alloy-600K.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
${OPENMD_HOME}/bin/Dump2XYZ -i Au-core-Ag-shell-800K.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
${OPENMD_HOME}/bin/Dump2XYZ -i Ag-core-Au-shell-800K.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
${OPENMD_HOME}/bin/Dump2XYZ -i vacancy_interface-800K.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
${OPENMD_HOME}/bin/Dump2XYZ -i vacancy_alloy-900K.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
${OPENMD_HOME}/bin/Dump2XYZ -i gold_fccrod.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
${OPENMD_HOME}/bin/Dump2XYZ -i gold_pentrod.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 --ico -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
${OPENMD_HOME}/bin/Dump2XYZ -i gold_ico_300K.md
#
#Example 12:
# Builds a regular decahedral nanoparticle from the <MetaData> block in gold.md
# using a 10 shells, and a lattice constant of 4.08 angstroms.
# Places the output (which can be used to start an OpenMD job) in 
# gold_deca.md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
${OPENMD_HOME}/bin/icosahedralBuilder --deca -o gold_deca.md --shells=10 --latticeConstant=4.08 gold.md
${OPENMD_HOME}/bin/thermalizer -o gold_deca_300.md -t 300 gold_deca.md
${OPENMD_HOME}/bin/Dump2XYZ -i gold_deca_300.md
#
#Example 13:
# Builds a ino-decahedral nanorod from the <MetaData> block in gold.md
# using a 10 shells, 5 atoms along the twin boundary, 100 atoms along the 
# column axis, and a lattice constant of 4.08 angstroms.
# Places the output (which can be used to start an OpenMD job) in 
# penta_rod.md 
#
# Note that builders will rewrite the number of molecules in each component
# to match the number of lattice sites.
#
${OPENMD_HOME}/bin/icosahedralBuilder --ino --columnAtoms=100 --twinAtoms=5 --shells=10 -d 4.08 -o penta_rod.md gold.md
${OPENMD_HOME}/bin/thermalizer -o gold_penta_rod_300.md -t 300 penta_rod.md
${OPENMD_HOME}/bin/Dump2XYZ -i gold_penta_rod_300.md
Revision:	1978
Committed:	Thu Mar 13 13:03:11 2014 UTC (11 years, 2 months ago) by gezelter
File size:	9217 byte(s)
Log Message:	More error message clarifications, added a few steps to the builders sample
#	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	1978	${OPENMD_HOME}/bin/Dump2XYZ -i FCC-100K.md
28	gezelter	1067	#
29			# Example 2:
30	gezelter	1066	# Builds an FCC lattice from the <MetaData> block in three_component.md
31			# uses 4 unit cells in each direction, a density of 1.0 g / cm^3, and
32			# molFractions of 0.4, 0.4, and 0.2 for the three components. Places
33	gezelter	1390	# the output (which can be used to start an OpenMD job) in random_FCC.md
34	gezelter	1066	#
35			# Note that builders will rewrite the number of molecules in each component
36			# to match the number of lattice sites.
37			#
38	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
39			${OPENMD_HOME}/bin/thermalizer -o random_FCC-100K.md -t 100 random_FCC.md
40	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i random_FCC-100K.md
41	gezelter	1076	#
42			# Example 3:
43			# Builds a spherical nanoparticle (FCC) from the <MetaData> block in gold.md
44			# using a particle radius of 30 Angstroms, and a lattice constant of 4.09
45	gezelter	1390	# angstroms. Places the output (which can be used to start an OpenMD job) in
46	gezelter	1076	# gold_sphere.md
47			#
48			# Note that builders will rewrite the number of molecules in each component
49			# to match the number of lattice sites.
50			#
51	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o gold_sphere.md --radius=30.0 --latticeConstant=4.09 gold.md
52			${OPENMD_HOME}/bin/thermalizer -o gold_sphere-500K.md -t 500.0 gold_sphere.md
53	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i gold_sphere-500K.md
54	gezelter	1076	#
55			# Example 4:
56			# Builds a random alloy spherical nanoparticle (FCC) from the <MetaData>
57			# block in bimetallic.md using a particle radius of 30 Angstroms, a
58			# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4.
59	gezelter	1390	# Places the output (which can be used to start an OpenMD job) in
60	gezelter	1076	# Au_Ag_alloy.md
61			#
62			# Note that builders will rewrite the number of molecules in each component
63			# to match the number of lattice sites.
64			#
65	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o Au_Ag_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 bimetallic.md
66			${OPENMD_HOME}/bin/thermalizer -o Au_Ag_alloy-600K.md -t 600 Au_Ag_alloy.md
67	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i Au_Ag_alloy-600K.md
68	gezelter	1076	#
69			# Example 5:
70			# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData>
71			# block in bimetallic.md using a particle radius of 25 Angstroms, a
72			# lattice constant of 4.09 angstroms, and a core radius for the gold atoms
73			# of 12.5 angstroms. Places the output (which can be used to start an
74	gezelter	1390	# OpenMD job) in Au(core)-Ag(shell).md
75	gezelter	1076	#
76			# Note that builders will rewrite the number of molecules in each component
77			# to match the number of lattice sites.
78			#
79	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o Au-core-Ag-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=12.5 bimetallic.md
80			${OPENMD_HOME}/bin/thermalizer -o Au-core-Ag-shell-800K.md -t 800.0 Au-core-Ag-shell.md
81	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i Au-core-Ag-shell-800K.md
82	gezelter	1076	#
83			# Example 6:
84			# Reverses example 5 by building a Ag(core)-Au(shell) spherical nanoparticle.
85			# Uses the same <MetaData> block from bimetallic.md,
86			# a particle radius of 25 Angstroms, a lattice constant of 4.09 angstroms,
87			# and a core radius for the silver atoms of 12.5 angstroms.
88	gezelter	1390	# Places the output (which can be used to start an OpenMD job) in
89	gezelter	1076	# Ag(core)-Au(shell).md
90			#
91			# Note that the last radius in Example 5 was taken as the particle radius,
92			# but since the components are reversed in this example, both are specified:
93			#
94			#
95	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
96			${OPENMD_HOME}/bin/thermalizer -o Ag-core-Au-shell-800K.md -t 800.0 Ag-core-Au-shell.md
97	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i Ag-core-Au-shell-800K.md
98	gezelter	1076	#
99			# Example 7:
100			# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData>
101			# block in bimetallic.md using a particle radius of 25 Angstroms, a
102			# lattice constant of 4.09 angstroms, and a core radius for the gold atoms
103			# of 12.5 angstroms. Places the output (which can be used to start an
104	gezelter	1390	# OpenMD job) in Au(core)-Ag(shell).md
105	gezelter	1076	#
106			# This example also introduces 70% vacancies in a 6 angstrom radial band
107			# around the bimetallic interface:
108			#
109	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
110			${OPENMD_HOME}/bin/thermalizer -o vacancy_interface-800K.md -t 800 vacancy_interface.md
111	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i vacancy_interface-800K.md
112	gezelter	1076	#
113			# Example 8:
114			# Builds a random alloy spherical nanoparticle with 30% vacancies using the
115			# <MetaData> block in bimetallic.md, a particle radius of 30 Angstroms, a
116			# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4.
117	gezelter	1390	# Places the output (which can be used to start an OpenMD job) in
118	gezelter	1076	# vacancy_alloy.md
119			#
120	gezelter	1805	${OPENMD_HOME}/bin/nanoparticleBuilder -o vacancy_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 --vacancyPercent=80 bimetallic.md
121			${OPENMD_HOME}/bin/thermalizer -o vacancy_alloy-900K.md -t 900 vacancy_alloy.md
122	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i vacancy_alloy-900K.md
123	gezelter	1782	#
124			#Example 9:
125			# Builds a spherically-capped nanorod (FCC) from the <MetaData> block in gold.md
126			# using a nanorod radius of 20 Angstroms, a length of 50 Angstroms and a lattice constant of 4.08
127			# angstroms. Places the output (which can be used to start an OpenMD job) in
128			# gold_fccrod.md
129			#
130			# Note that builders will rewrite the number of molecules in each component
131			# to match the number of lattice sites.
132			#
133	gezelter	1805	${OPENMD_HOME}/bin/nanorodBuilder -o gold_fccrod.md --radius=20.0 --length=50.0 --latticeConstant=4.08 gold.md
134	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i gold_fccrod.md
135	gezelter	1782	#
136			#Example 10:
137			# Builds a pentagonal nanorod from the <MetaData> block in gold.md
138			# using a nanorod radius of 15 Angstroms, a length of 64 Angstroms and a lattice constant of 4.08
139			# angstroms. Places the output (which can be used to start an OpenMD job) in
140			# gold_pentrod.md
141			#
142			# Note that builders will rewrite the number of molecules in each component
143			# to match the number of lattice sites.
144			#
145	gezelter	1805	${OPENMD_HOME}/bin/nanorod_pentBuilder -o gold_pentrod.md --radius=15.0 --length=64.0 --latticeConstant=4.08 gold.md
146	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i gold_pentrod.md
147	gezelter	1886	#
148			#Example 11:
149			# Builds a Mackay icosahedral nanoparticle from the <MetaData> block in gold.md
150			# using a 8 shells, and a lattice constant of 4.08 angstroms.
151			# Places the output (which can be used to start an OpenMD job) in
152			# gold_ico.md
153			#
154			# Note that builders will rewrite the number of molecules in each component
155			# to match the number of lattice sites.
156			#
157	gezelter	1978	${OPENMD_HOME}/bin/icosahedralBuilder --ico -o gold_ico.md --shells=8 --latticeConstant=4.08 gold.md
158	gezelter	1886	${OPENMD_HOME}/bin/thermalizer -o gold_ico_300K.md -t 300 gold_ico.md
159	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i gold_ico_300K.md
160	gezelter	1950	#
161			#Example 12:
162			# Builds a regular decahedral nanoparticle from the <MetaData> block in gold.md
163			# using a 10 shells, and a lattice constant of 4.08 angstroms.
164			# Places the output (which can be used to start an OpenMD job) in
165			# gold_deca.md
166			#
167			# Note that builders will rewrite the number of molecules in each component
168			# to match the number of lattice sites.
169			#
170	gezelter	1978	${OPENMD_HOME}/bin/icosahedralBuilder --deca -o gold_deca.md --shells=10 --latticeConstant=4.08 gold.md
171	gezelter	1950	${OPENMD_HOME}/bin/thermalizer -o gold_deca_300.md -t 300 gold_deca.md
172	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i gold_deca_300.md
173	gezelter	1950	#
174			#Example 13:
175			# Builds a ino-decahedral nanorod from the <MetaData> block in gold.md
176			# using a 10 shells, 5 atoms along the twin boundary, 100 atoms along the
177			# column axis, and a lattice constant of 4.08 angstroms.
178			# Places the output (which can be used to start an OpenMD job) in
179			# penta_rod.md
180			#
181			# Note that builders will rewrite the number of molecules in each component
182			# to match the number of lattice sites.
183			#
184			${OPENMD_HOME}/bin/icosahedralBuilder --ino --columnAtoms=100 --twinAtoms=5 --shells=10 -d 4.08 -o penta_rod.md gold.md
185			${OPENMD_HOME}/bin/thermalizer -o gold_penta_rod_300.md -t 300 penta_rod.md
186	gezelter	1978	${OPENMD_HOME}/bin/Dump2XYZ -i gold_penta_rod_300.md