| 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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i FCC-100K.md |
| 28 |
|
# |
| 29 |
|
# Example 2: |
| 30 |
|
# Builds an FCC lattice from the <MetaData> block in three_component.md |
| 37 |
|
# |
| 38 |
|
${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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i random_FCC-100K.md |
| 41 |
|
# |
| 42 |
|
# Example 3: |
| 43 |
|
# Builds a spherical nanoparticle (FCC) from the <MetaData> block in gold.md |
| 50 |
|
# |
| 51 |
|
${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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i gold_sphere-500K.md |
| 54 |
|
# |
| 55 |
|
# Example 4: |
| 56 |
|
# Builds a random alloy spherical nanoparticle (FCC) from the <MetaData> |
| 64 |
|
# |
| 65 |
|
${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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i Au_Ag_alloy-600K.md |
| 68 |
|
# |
| 69 |
|
# Example 5: |
| 70 |
|
# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData> |
| 78 |
|
# |
| 79 |
|
${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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i Au-core-Ag-shell-800K.md |
| 82 |
|
# |
| 83 |
|
# Example 6: |
| 84 |
|
# Reverses example 5 by building a Ag(core)-Au(shell) spherical nanoparticle. |
| 94 |
|
# |
| 95 |
|
${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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i Ag-core-Au-shell-800K.md |
| 98 |
|
# |
| 99 |
|
# Example 7: |
| 100 |
|
# Builds a Au(core)-Ag(shell) spherical nanoparticle (FCC) from the <MetaData> |
| 108 |
|
# |
| 109 |
|
${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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i vacancy_interface-800K.md |
| 112 |
|
# |
| 113 |
|
# Example 8: |
| 114 |
|
# Builds a random alloy spherical nanoparticle with 30% vacancies using the |
| 119 |
|
# |
| 120 |
|
${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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i vacancy_alloy-900K.md |
| 123 |
|
# |
| 124 |
|
#Example 9: |
| 125 |
|
# Builds a spherically-capped nanorod (FCC) from the <MetaData> block in gold.md |
| 131 |
|
# to match the number of lattice sites. |
| 132 |
|
# |
| 133 |
|
${OPENMD_HOME}/bin/nanorodBuilder -o gold_fccrod.md --radius=20.0 --length=50.0 --latticeConstant=4.08 gold.md |
| 134 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i gold_fccrod.md |
| 135 |
|
# |
| 136 |
|
#Example 10: |
| 137 |
|
# Builds a pentagonal nanorod from the <MetaData> block in gold.md |
| 143 |
|
# to match the number of lattice sites. |
| 144 |
|
# |
| 145 |
|
${OPENMD_HOME}/bin/nanorod_pentBuilder -o gold_pentrod.md --radius=15.0 --length=64.0 --latticeConstant=4.08 gold.md |
| 146 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i gold_pentrod.md |
| 147 |
|
# |
| 148 |
|
#Example 11: |
| 149 |
|
# Builds a Mackay icosahedral nanoparticle from the <MetaData> block in gold.md |
| 154 |
|
# Note that builders will rewrite the number of molecules in each component |
| 155 |
|
# to match the number of lattice sites. |
| 156 |
|
# |
| 157 |
< |
${OPENMD_HOME}/bin/icosahedralBuilder -o gold_ico.md --shells=8 --latticeConstant=4.08 gold.md |
| 157 |
> |
${OPENMD_HOME}/bin/icosahedralBuilder --ico -o gold_ico.md --shells=8 --latticeConstant=4.08 gold.md |
| 158 |
|
${OPENMD_HOME}/bin/thermalizer -o gold_ico_300K.md -t 300 gold_ico.md |
| 159 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i gold_ico_300K.md |
| 160 |
|
# |
| 161 |
|
#Example 12: |
| 162 |
|
# Builds a regular decahedral nanoparticle from the <MetaData> block in gold.md |
| 167 |
|
# Note that builders will rewrite the number of molecules in each component |
| 168 |
|
# to match the number of lattice sites. |
| 169 |
|
# |
| 170 |
< |
${OPENMD_HOME}/bin/icosahedralBuilder -o gold_deca.md --shells=10 --latticeConstant=4.08 gold.md |
| 170 |
> |
${OPENMD_HOME}/bin/icosahedralBuilder --deca -o gold_deca.md --shells=10 --latticeConstant=4.08 gold.md |
| 171 |
|
${OPENMD_HOME}/bin/thermalizer -o gold_deca_300.md -t 300 gold_deca.md |
| 172 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i gold_deca_300.md |
| 173 |
|
# |
| 174 |
|
#Example 13: |
| 175 |
|
# Builds a ino-decahedral nanorod from the <MetaData> block in gold.md |
| 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 |
+ |
${OPENMD_HOME}/bin/Dump2XYZ -i gold_penta_rod_300.md |
