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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13674 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-07-22 15:26:43 +00:00
parent 60cd71620a
commit 63802b7688
8 changed files with 18417 additions and 0 deletions
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35
examples/USER/diffraction/BulkNi.in Normal file
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variable A string bulkNi
log $A.log
boundary p p p
units metal
timestep 0.001
lattice fcc 3.52
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style none
mass * 58.71
atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.05 echo manual
fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] weights c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
dump 1 all custom 1 $A.dump id x y z
run 0
unfix 1
unfix 2
uncompute XRD
uncompute SAED

35
examples/USER/diffraction/Output/BulkNi.in Normal file
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variable A string bulkNi
log $A.log
boundary p p p
units metal
timestep 0.001
lattice fcc 3.52
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style none
mass * 58.71
atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 &
Zone 0 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.01 echo manual
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
dump 1 all custom 1 $A.dump id x y z
run 0
unfix 1
unfix 2
uncompute XRD
uncompute SAED

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examples/USER/diffraction/Output/bulkNi.hist.xrd.correct Normal file
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# Histogrammed data for fix 1
# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
# Bin Coord Count Count/Total
0 200 2.11404e+09 0 40.0105 79.9779
1 40.1 3.06101e-21 1.44795e-30
2 40.3 1.30992e-21 6.19629e-31
3 40.5 2.98726e-21 1.41306e-30
4 40.7 9.05005e-22 4.28094e-31
5 40.9 1.1445e-21 5.41384e-31
6 41.1 3.04226e-21 1.43908e-30
7 41.3 1.60531e-21 7.59359e-31
8 41.5 1.14896e-21 5.43489e-31
9 41.7 7.59155e-21 3.59102e-30
10 41.9 1.66096e-21 7.85684e-31
11 42.1 3.78317e-21 1.78955e-30
12 42.3 4.20832e-21 1.99066e-30
13 42.5 2.20707e-21 1.04401e-30
14 42.7 1.36704e-21 6.4665e-31
15 42.9 1.6698e-21 7.89864e-31
16 43.1 4.3614e-21 2.06307e-30
17 43.3 1.40184e-21 6.63112e-31
18 43.5 1.10104e-21 5.20826e-31
19 43.7 9.01097e-21 4.26245e-30
20 43.9 1.47616e-21 6.98269e-31
21 44.1 2.10253e-21 9.94555e-31
22 44.3 2.59795e-21 1.22891e-30
23 44.5 1.22201e+09 0.578046
24 44.7 1.23743e-21 5.85339e-31
25 44.9 3.9512e-21 1.86903e-30
26 45.1 1.6662e-21 7.88163e-31
27 45.3 1.87555e-21 8.87188e-31
28 45.5 7.78421e-22 3.68216e-31
29 45.7 2.56826e-21 1.21486e-30
30 45.9 1.28976e-21 6.10092e-31
31 46.1 2.44543e-21 1.15676e-30
32 46.3 6.65824e-21 3.14954e-30
33 46.5 1.0233e-20 4.84049e-30
34 46.7 9.00075e-22 4.25762e-31
35 46.9 2.32255e-21 1.09864e-30
36 47.1 6.14619e-21 2.90732e-30
37 47.3 3.37255e-21 1.59531e-30
38 47.5 2.90858e-21 1.37584e-30
39 47.7 2.52643e-21 1.19507e-30
40 47.9 2.2425e-21 1.06077e-30
41 48.1 2.0611e-21 9.74959e-31
42 48.3 3.02792e-21 1.43229e-30
43 48.5 4.569e-21 2.16127e-30
44 48.7 1.36212e-21 6.4432e-31
45 48.9 2.3294e-21 1.10188e-30
46 49.1 1.25221e-20 5.92332e-30
47 49.3 4.08541e-21 1.93252e-30
48 49.5 1.40201e-21 6.6319e-31
49 49.7 1.42613e-21 6.74603e-31
50 49.9 2.43896e-21 1.1537e-30
51 50.1 2.04129e-21 9.65589e-31
52 50.3 2.20722e-21 1.04408e-30
53 50.5 8.97318e-22 4.24458e-31
54 50.7 1.33863e-21 6.33211e-31
55 50.9 5.85528e-21 2.76972e-30
56 51.1 2.165e-21 1.02411e-30
57 51.3 2.81994e-21 1.33392e-30
58 51.5 1.28923e-21 6.09844e-31
59 51.7 1.47388e-20 6.97188e-30
60 51.9 5.68489e+08 0.268912
61 52.1 2.83688e-21 1.34193e-30
62 52.3 4.83659e-21 2.28785e-30
63 52.5 9.80481e-22 4.63796e-31
64 52.7 1.58455e-21 7.49539e-31
65 52.9 1.41338e-21 6.68571e-31
66 53.1 7.3765e-21 3.4893e-30
67 53.3 1.64796e-21 7.79532e-31
68 53.5 8.93791e-22 4.22789e-31
69 53.7 3.99056e-21 1.88765e-30
70 53.9 5.52716e-21 2.61451e-30
71 54.1 2.82704e-21 1.33727e-30
72 54.3 1.84486e-21 8.72672e-31
73 54.5 1.81266e-21 8.57442e-31
74 54.7 5.48984e-21 2.59685e-30
75 54.9 7.84523e-22 3.71102e-31
76 55.1 1.57143e-21 7.43331e-31
77 55.3 2.54241e-21 1.20263e-30
78 55.5 1.63581e-21 7.73785e-31
79 55.7 7.65899e-21 3.62292e-30
80 55.9 3.12447e-21 1.47797e-30
81 56.1 3.95637e-21 1.87148e-30
82 56.3 9.84993e-21 4.6593e-30
83 56.5 1.71247e-21 8.10049e-31
84 56.7 1.31922e-21 6.24028e-31
85 56.9 1.80226e-21 8.52523e-31
86 57.1 1.20821e-21 5.71519e-31
87 57.3 2.49994e-21 1.18255e-30
88 57.5 2.16549e-21 1.02434e-30
89 57.7 4.12784e-21 1.95259e-30
90 57.9 5.48851e-21 2.59622e-30
91 58.1 5.63823e-21 2.66705e-30
92 58.3 1.0585e-21 5.00701e-31
93 58.5 1.79708e-21 8.5007e-31
94 58.7 2.1958e-21 1.03868e-30
95 58.9 1.45819e-21 6.89766e-31
96 59.1 2.57536e-21 1.21822e-30
97 59.3 1.60719e-21 7.60246e-31
98 59.5 6.5472e-21 3.09701e-30
99 59.7 2.07096e-21 9.79624e-31
100 59.9 2.6863e-21 1.2707e-30
101 60.1 9.15437e-21 4.33028e-30
102 60.3 1.32576e-21 6.27121e-31
103 60.5 6.43633e-21 3.04457e-30
104 60.7 1.53423e-21 7.25737e-31
105 60.9 1.65585e-21 7.83267e-31
106 61.1 1.3262e-21 6.27329e-31
107 61.3 1.19095e-21 5.63354e-31
108 61.5 6.54555e-21 3.09623e-30
109 61.7 1.60052e-21 7.57092e-31
110 61.9 2.89841e-21 1.37103e-30
111 62.1 5.64558e-21 2.67052e-30
112 62.3 1.5428e-21 7.29791e-31
113 62.5 4.63824e-21 2.19402e-30
114 62.7 1.40301e-21 6.63666e-31
115 62.9 3.78799e-21 1.79183e-30
116 63.1 7.1128e-22 3.36456e-31
117 63.3 8.35823e-22 3.95368e-31
118 63.5 9.4629e-21 4.47622e-30
119 63.7 2.28075e-21 1.07886e-30
120 63.9 2.78324e-21 1.31655e-30
121 64.1 2.47584e-21 1.17114e-30
122 64.3 9.22547e-22 4.36391e-31
123 64.5 2.14799e-21 1.01606e-30
124 64.7 3.12863e-21 1.47993e-30
125 64.9 1.68285e-21 7.96037e-31
126 65.1 3.35452e-21 1.58678e-30
127 65.3 3.32631e-21 1.57344e-30
128 65.5 1.60713e-21 7.6022e-31
129 65.7 1.73875e-21 8.22479e-31
130 65.9 2.17604e-21 1.02933e-30
131 66.1 7.56798e-21 3.57987e-30
132 66.3 1.37838e-21 6.52016e-31
133 66.5 1.51962e-21 7.18824e-31
134 66.7 1.52794e-21 7.22761e-31
135 66.9 2.59611e-21 1.22804e-30
136 67.1 8.44384e-22 3.99418e-31
137 67.3 4.97545e-21 2.35353e-30
138 67.5 1.74409e-21 8.25005e-31
139 67.7 1.0864e-21 5.13901e-31
140 67.9 2.78129e-21 1.31563e-30
141 68.1 2.79776e-21 1.32342e-30
142 68.3 7.89266e-21 3.73345e-30
143 68.5 1.92037e-21 9.08391e-31
144 68.7 1.24465e-21 5.88756e-31
145 68.9 1.13109e-21 5.35039e-31
146 69.1 3.30078e-21 1.56136e-30
147 69.3 1.69411e-21 8.01364e-31
148 69.5 3.97153e-21 1.87865e-30
149 69.7 2.17947e-21 1.03095e-30
150 69.9 1.38947e-20 6.57257e-30
151 70.1 3.63321e-21 1.71861e-30
152 70.3 1.15347e-21 5.45625e-31
153 70.5 9.98105e-22 4.72133e-31
154 70.7 2.05654e-21 9.72803e-31
155 70.9 1.02154e-21 4.83217e-31
156 71.1 3.2996e-21 1.5608e-30
157 71.3 8.58913e-22 4.06291e-31
158 71.5 1.68647e-21 7.97747e-31
159 71.7 5.59365e-21 2.64596e-30
160 71.9 5.16255e-21 2.44203e-30
161 72.1 1.22278e-21 5.78412e-31
162 72.3 6.20724e-21 2.9362e-30
163 72.5 4.35919e-21 2.06202e-30
164 72.7 1.81512e-21 8.58606e-31
165 72.9 2.90474e-21 1.37403e-30
166 73.1 1.77488e-21 8.39571e-31
167 73.3 1.03662e-21 4.9035e-31
168 73.5 3.9255e-21 1.85688e-30
169 73.7 1.42352e-21 6.73366e-31
170 73.9 1.32264e-21 6.25646e-31
171 74.1 1.00356e-21 4.74713e-31
172 74.3 7.42958e-21 3.51441e-30
173 74.5 4.42913e-22 2.09511e-31
174 74.7 2.76147e-21 1.30626e-30
175 74.9 1.0997e-21 5.20188e-31
176 75.1 5.57998e-21 2.63949e-30
177 75.3 1.06529e-21 5.03911e-31
178 75.5 5.08497e-21 2.40534e-30
179 75.7 3.74671e-21 1.7723e-30
180 75.9 1.19614e-21 5.6581e-31
181 76.1 5.02708e-22 2.37796e-31
182 76.3 1.26833e-21 5.99957e-31
183 76.5 3.23536e+08 0.153042
184 76.7 2.10049e-21 9.93592e-31
185 76.9 7.24942e-22 3.42919e-31
186 77.1 1.59221e-21 7.53162e-31
187 77.3 3.93047e-21 1.85923e-30
188 77.5 2.50976e-21 1.18719e-30
189 77.7 1.71235e-21 8.09991e-31
190 77.9 4.51362e-21 2.13507e-30
191 78.1 7.26497e-22 3.43654e-31
192 78.3 2.50185e-21 1.18345e-30
193 78.5 1.75672e-21 8.3098e-31
194 78.7 4.01584e-22 1.89961e-31
195 78.9 3.68006e-21 1.74078e-30
196 79.1 6.27868e-21 2.97e-30
197 79.3 4.54647e-21 2.15061e-30
198 79.5 1.47372e-21 6.97114e-31
199 79.7 1.35649e-21 6.41658e-31
200 79.9 8.07703e-22 3.82067e-31

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examples/USER/diffraction/Output/bulkNi.log.correct Normal file
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boundary p p p
units metal
timestep 0.001
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
2 by 2 by 4 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style none
mass * 58.71
atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 dR_Ewald 0.05 echo manual
fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] weights c_XRD[2] mode vector file $A.hist.xrd
fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] weights c_XRD[2] mode vector file bulkNi.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
fix 2 all saed/vtk 1 1 1 c_SAED file bulkNi_001.saed
dump 1 all custom 1 $A.dump id x y z
dump 1 all custom 1 bulkNi.dump id x y z
run 0
Memory usage per processor = 9.6642 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
Loop time of 1.30087e-05 on 16 procs for 0 steps with 32000 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 1.30087e-05 (100)
Nlocal: 2000 ave 2200 max 1800 min
Histogram: 4 0 0 0 0 8 0 0 0 4
Nghost: 370.75 ave 426 max 226 min
Histogram: 4 0 0 0 0 0 0 0 4 8
Neighs: 0 ave 0 max 0 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
uncompute XRD
uncompute SAED
Please see the log.cite file for references relevant to this simulation

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This LAMMPS simulation made specific use of work described in the
following references. See http://lammps.sandia.gov/cite.html
for details.
compute_xrd command:
@Article{Coleman13,
author = {S. P. Coleman, D. E. Spearot, L. Capolungo},
title = {Virtual diffraction analysis of Ni [010] symmetric tilt grain boundaries},
journal = {Modelling and Simulation in Materials Science and Engineering},
year = 2013,
volume = 21,
pages = {055020}
}
compute_saed command:
@Article{Coleman13,
author = {S. P. Coleman, D. E. Spearot, L. Capolungo},
title = {Virtual diffraction analysis of Ni [010] symmetric tilt grain boundaries},
journal = {Modelling and Simulation in Materials Science and Engineering},
year = 2013,
volume = 21,
pages = {055020}
}

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This is a simple example of showing the computation of virutal x-ray
and electron diffraction patterns for Ni.
In addition to the LAMMPS output, a simple visualizaiton of the electron
diffraction data is included. The visualization was created using the VisIt
Open Source visualiztion software develeoped at Larrence Livermore National
Laboraatory (https://wci.llnl.gov/simulation/computer-codes/visit/).
Below is a step by step guide to produce similar images:
a) Open the diffraction .vtk files in VisIt
b) Click add->pseudocolor->intensity;
*Note, green name means its ready to be drawn
c) Click Draw;
*Note, you will see the full rectangular mesh grid which is what we
are wanting.
We need to remove ghost data (those values set to -1).
d) Select intensity plot;
Click Operators->Selection->Isovolume;
Double click isovolume (under intensity plot);
Change lower bound to 0;
Click Apply;
Click Dismiss;
Click Draw;
 
*Note, now you will see only where there was valid intensity data (if you
don't use Zone it will be a sphere).  But most intensity are low so color
the intensity by log scale.
e) Select intensity plot
Double click Pseudocolor;
Change Scale to Log;
Check Mimimum Limit;
Input non-zero minimum limit (i.e. 1);
Click Apply;
Click Dismiss;
Note, clicking apply will change the scale automatically.  But unless
you have used Zone and a thin dR_Ewald you likely have lots of extra
data visualized that does not intersect the Ewald sphere.  Next, we
want to take a spherical slice to mimic the intersection of Ewald's
sphere with reciprocal space.
f) Select intensity plot;
Click Operators->Slicing>Spherical Slice;
Double click Spherical Slice;
Change the origin/radius to represent the center of your Ewald sphere;
**(i.e. 39.84063 0 0) and radius (i.e. 39.84063) for lambda = 0.251 **
Click Apply;
Click Dismiss;
Click Draw;
This is the saed pattern, but we are not guaranteed to be aligned correctly
with the zone axis.
g) On the menu bar... select Controls -> View;
Change View Normal to the zone axis of choice (i.e. -1 0 0);
Adjust Up Vector if desired (i.e. 0 1 0);
Turn off Perspective view;
Click Apply;
Click Dismiss;
*Note that for the primary x, y, and z zone axis you can use the drop
own Align to axis.  However, it is likely that there is a bunch of extra
annotations on the image that don't look appealing.
h) On the menu bar... select Control-> Annotation;
*Here you can change what is visualized along side the data and how
you display axis information.  I typically turn most all the display
information off.
i) Save the image
Click File-> Set save options
Click Save
** Note, further fine tuning can be achieved by adjusing the color table and
max/min values **