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Comparing trunk/samples/builders/runMe (file contents):
Revision 1079 by gezelter, Thu Oct 19 15:57:07 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1   #!/bin/sh
2   #
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 < # The velocitizer command takes the FCC.md file and resamples the velocities
22 > # The thermalizer command takes the FCC.md file and resamples the velocities
23   # from a Maxwell-Boltzmann distribution set to 100K:
24   #
25   ../../bin/simpleBuilder -o FCC.md --nx=5 --ny=5 --nz=5 --density=1.0 one_component.md
26 < ../../bin/velocitizer -o FCC-100K.md -t 100 FCC.md
26 > ../../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
38 < ../../bin/velocitizer -o random_FCC-100K.md -t 100 random_FCC.md
38 > ../../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
50 < ../../bin/velocitizer -o gold_sphere-500K.md -t 500.0 gold_sphere.md
50 > ../../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
63 < ../../bin/velocitizer -o Au_Ag_alloy-600K.md -t 600 Au_Ag_alloy.md
63 > ../../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
76 < ../../bin/velocitizer -o Au-core-Ag-shell-800K.md -t 800.0 Au-core-Ag-shell.md
76 > ../../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,
# Line 88 | Line 88
88   #
89   #
90   ../../bin/nanoparticleBuilder -o Ag-core-Au-shell.md --radius=30.0 --latticeConstant=4.09 --shellRadius=30.0,12.5 bimetallic.md
91 < ../../bin/velocitizer -o Ag-core-Au-shell-800K.md -t 800.0 Ag-core-Au-shell.md
91 > ../../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
104 < ../../bin/velocitizer -o vacancy_interface-800K.md -t 800 vacancy_interface.md
104 > ../../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
114 < ../../bin/velocitizer -o vacancy_alloy-900K.md -t 900 vacancy_alloy.md
114 > ../../bin/thermalizer -o vacancy_alloy-900K.md -t 900 vacancy_alloy.md

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