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#!/bin/sh |
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OPENMD_HOME=@CMAKE_INSTALL_PREFIX@ |
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# This is a collection of sample commands that can be used to build |
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# OpenMD start files. In OpenMD, the start files have a <MetaData> |
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# block to give information about the kind of simulation being performed. |
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# The start files also contain at least one <Snapshot> block which contains |
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# information about the instantaneous configuration. |
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# |
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# One of the difficult tasks in using any simulation program is figuring |
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# out how to format the start file correctly. OpenMD includes a set of |
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# "builder" programs to make that process a bit less painful. |
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# |
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# Example 1: |
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# Builds an FCC lattice from the <MetaData> block in one_component.md |
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# Uses 5 unit cells in each direction, a density of 1.0 g / cm^3, and |
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# places the output (which can be used to start an OpenMD job) in |
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# FCC.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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# The thermalizer command takes the FCC.md file and resamples the velocities |
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# from a Maxwell-Boltzmann distribution set to 100K: |
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# |
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${OPENMD_HOME}/bin/simpleBuilder -o FCC.md --nx=5 --ny=5 --nz=5 --density=1.0 one_component.md |
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${OPENMD_HOME}/bin/thermalizer -o FCC-100K.md -t 100 FCC.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i FCC-100K.md |
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# |
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# Example 2: |
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# Builds an FCC lattice from the <MetaData> block in three_component.md |
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# uses 4 unit cells in each direction, a density of 1.0 g / cm^3, and |
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# molFractions of 0.4, 0.4, and 0.2 for the three components. Places |
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# the output (which can be used to start an OpenMD job) in random_FCC.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${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 |
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${OPENMD_HOME}/bin/thermalizer -o random_FCC-100K.md -t 100 random_FCC.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i random_FCC-100K.md |
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# |
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# Example 3: |
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# Builds a spherical nanoparticle (FCC) from the <MetaData> block in gold.md |
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# using a particle radius of 30 Angstroms, and a lattice constant of 4.09 |
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# angstroms. Places the output (which can be used to start an OpenMD job) in |
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# gold_sphere.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${OPENMD_HOME}/bin/nanoparticleBuilder -o gold_sphere.md --radius=30.0 --latticeConstant=4.09 gold.md |
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${OPENMD_HOME}/bin/thermalizer -o gold_sphere-500K.md -t 500.0 gold_sphere.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i gold_sphere-500K.md |
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# |
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# Example 4: |
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# Builds a random alloy spherical nanoparticle (FCC) from the <MetaData> |
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# block in bimetallic.md using a particle radius of 30 Angstroms, a |
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# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4. |
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# Places the output (which can be used to start an OpenMD job) in |
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# Au_Ag_alloy.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${OPENMD_HOME}/bin/nanoparticleBuilder -o Au_Ag_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 bimetallic.md |
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${OPENMD_HOME}/bin/thermalizer -o Au_Ag_alloy-600K.md -t 600 Au_Ag_alloy.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i Au_Ag_alloy-600K.md |
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# |
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# Example 5: |
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# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData> |
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# block in bimetallic.md using a particle radius of 25 Angstroms, a |
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# lattice constant of 4.09 angstroms, and a core radius for the gold atoms |
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# of 12.5 angstroms. Places the output (which can be used to start an |
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# OpenMD job) in Au(core)-Ag(shell).md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${OPENMD_HOME}/bin/nanoparticleBuilder -o Au-core-Ag-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=12.5 bimetallic.md |
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${OPENMD_HOME}/bin/thermalizer -o Au-core-Ag-shell-800K.md -t 800.0 Au-core-Ag-shell.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i Au-core-Ag-shell-800K.md |
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# |
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# Example 6: |
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# Reverses example 5 by building a Ag(core)-Au(shell) spherical nanoparticle. |
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# Uses the same <MetaData> block from bimetallic.md, |
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# a particle radius of 25 Angstroms, a lattice constant of 4.09 angstroms, |
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# and a core radius for the silver atoms of 12.5 angstroms. |
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# Places the output (which can be used to start an OpenMD job) in |
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# Ag(core)-Au(shell).md |
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# |
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# Note that the last radius in Example 5 was taken as the particle radius, |
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# but since the components are reversed in this example, both are specified: |
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# |
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# |
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${OPENMD_HOME}/bin/nanoparticleBuilder -o Ag-core-Au-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=30.0,12.5 bimetallic.md |
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${OPENMD_HOME}/bin/thermalizer -o Ag-core-Au-shell-800K.md -t 800.0 Ag-core-Au-shell.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i Ag-core-Au-shell-800K.md |
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# |
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# Example 7: |
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# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData> |
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# block in bimetallic.md using a particle radius of 25 Angstroms, a |
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# lattice constant of 4.09 angstroms, and a core radius for the gold atoms |
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# of 12.5 angstroms. Places the output (which can be used to start an |
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# OpenMD job) in Au(core)-Ag(shell).md |
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# |
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# This example also introduces 70% vacancies in a 6 angstrom radial band |
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# around the bimetallic interface: |
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# |
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${OPENMD_HOME}/bin/nanoparticleBuilder -o vacancy_interface.md --radius=20.0 --latticeConstant=4.09 --shellRadius=12.5 --vacancyPercent=70 --vacancyInnerRadius=9.5 --vacancyOuterRadius=15.5 bimetallic.md |
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${OPENMD_HOME}/bin/thermalizer -o vacancy_interface-800K.md -t 800 vacancy_interface.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i vacancy_interface-800K.md |
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# |
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# Example 8: |
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# Builds a random alloy spherical nanoparticle with 30% vacancies using the |
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# <MetaData> block in bimetallic.md, a particle radius of 30 Angstroms, a |
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# lattice constant of 4.09 angstroms, and a mole fraction for the gold of 0.4. |
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# Places the output (which can be used to start an OpenMD job) in |
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# vacancy_alloy.md |
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# |
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${OPENMD_HOME}/bin/nanoparticleBuilder -o vacancy_alloy.md --radius=30.0 --latticeConstant=4.09 --molFraction=0.4 --vacancyPercent=80 bimetallic.md |
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${OPENMD_HOME}/bin/thermalizer -o vacancy_alloy-900K.md -t 900 vacancy_alloy.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i vacancy_alloy-900K.md |
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# |
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#Example 9: |
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# Builds a spherically-capped nanorod (FCC) from the <MetaData> block in gold.md |
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# using a nanorod radius of 20 Angstroms, a length of 50 Angstroms and a lattice constant of 4.08 |
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# angstroms. Places the output (which can be used to start an OpenMD job) in |
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# gold_fccrod.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${OPENMD_HOME}/bin/nanorodBuilder -o gold_fccrod.md --radius=20.0 --length=50.0 --latticeConstant=4.08 gold.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i gold_fccrod.md |
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# |
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#Example 10: |
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# Builds a pentagonal nanorod from the <MetaData> block in gold.md |
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# using a nanorod radius of 15 Angstroms, a length of 64 Angstroms and a lattice constant of 4.08 |
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# angstroms. Places the output (which can be used to start an OpenMD job) in |
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# gold_pentrod.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${OPENMD_HOME}/bin/nanorod_pentBuilder -o gold_pentrod.md --radius=15.0 --length=64.0 --latticeConstant=4.08 gold.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i gold_pentrod.md |
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# |
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#Example 11: |
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# Builds a Mackay icosahedral nanoparticle from the <MetaData> block in gold.md |
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# using a 8 shells, and a lattice constant of 4.08 angstroms. |
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# Places the output (which can be used to start an OpenMD job) in |
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# gold_ico.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${OPENMD_HOME}/bin/icosahedralBuilder --ico -o gold_ico.md --shells=8 --latticeConstant=4.08 gold.md |
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${OPENMD_HOME}/bin/thermalizer -o gold_ico_300K.md -t 300 gold_ico.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i gold_ico_300K.md |
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# |
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#Example 12: |
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# Builds a regular decahedral nanoparticle from the <MetaData> block in gold.md |
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# using a 10 shells, and a lattice constant of 4.08 angstroms. |
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# Places the output (which can be used to start an OpenMD job) in |
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# gold_deca.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${OPENMD_HOME}/bin/icosahedralBuilder --deca -o gold_deca.md --shells=10 --latticeConstant=4.08 gold.md |
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${OPENMD_HOME}/bin/thermalizer -o gold_deca_300.md -t 300 gold_deca.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i gold_deca_300.md |
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# |
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#Example 13: |
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# Builds a ino-decahedral nanorod from the <MetaData> block in gold.md |
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# using a 10 shells, 5 atoms along the twin boundary, 100 atoms along the |
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# column axis, and a lattice constant of 4.08 angstroms. |
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# Places the output (which can be used to start an OpenMD job) in |
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# penta_rod.md |
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# |
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# Note that builders will rewrite the number of molecules in each component |
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# to match the number of lattice sites. |
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# |
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${OPENMD_HOME}/bin/icosahedralBuilder --ino --columnAtoms=100 --twinAtoms=5 --shells=10 -d 4.08 -o penta_rod.md gold.md |
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${OPENMD_HOME}/bin/thermalizer -o gold_penta_rod_300.md -t 300 penta_rod.md |
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${OPENMD_HOME}/bin/Dump2XYZ -i gold_penta_rod_300.md |
