| 1 |
|
#!/bin/sh |
| 2 |
< |
# |
| 2 |
> |
OPENMD_HOME=@CMAKE_INSTALL_PREFIX@ |
| 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> |
| 4 |
> |
# OpenMD start files. In OpenMD, 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 |
| 10 |
> |
# out how to format the start file correctly. OpenMD 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 |
| 16 |
> |
# places the output (which can be used to start an OpenMD 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 |
| 22 |
> |
# The thermalizer command takes the FCC.md file and resamples the velocities |
| 23 |
> |
# from a Maxwell-Boltzmann distribution set to 100K: |
| 24 |
|
# |
| 25 |
+ |
${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 |
+ |
# |
| 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 |
| 32 |
> |
# the output (which can be used to start an OpenMD 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 |
| 37 |
> |
${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 |
|
# |
| 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 |
| 43 |
> |
# angstroms. Places the output (which can be used to start an OpenMD 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 |
| 49 |
> |
${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 |
|
# |
| 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 |
| 56 |
> |
# Places the output (which can be used to start an OpenMD 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 |
| 62 |
> |
${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 |
|
# |
| 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 |
| 70 |
> |
# OpenMD 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 |
| 75 |
> |
${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 |
|
# |
| 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 |
| 83 |
> |
# Places the output (which can be used to start an OpenMD 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 |
| 90 |
> |
${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 |
|
# |
| 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 |
| 98 |
> |
# OpenMD 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 |
| 103 |
> |
${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 |
|
# |
| 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 |
| 110 |
> |
# Places the output (which can be used to start an OpenMD 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 |
| 113 |
> |
${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 |
> |
# |
| 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 |
> |
${OPENMD_HOME}/bin/nanorodBuilder -o gold_fccrod.md --radius=20.0 --length=50.0 --latticeConstant=4.08 gold.md |
| 126 |
> |
# |
| 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 |
> |
${OPENMD_HOME}/bin/nanorod_pentBuilder -o gold_pentrod.md --radius=15.0 --length=64.0 --latticeConstant=4.08 gold.md |
