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rLAMMPS lammps
vizinfo.py
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# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# vizinfo class, not a top-level Pizza.py tool
# History
# 8/05, Matt Jones (BYU): original version
# 9/05, Steve Plimpton: added 140-color table
# ToDo list
# Variables
# Imports and external programs
import
types
# Class definition
class
vizinfo
:
"""
Information holder for Pizza.py visualization tools
acolor,bcolor,tcolor,lcolor = RGB values for each atom/bond/tri/line type
arad = radius of each atom type
brad,lrad = thickness of each bond/line type
tfill = fill flag for each triangle type
all of these arrays are indexed by object type which runs 1-Ntype
nacolor,nbcolor,ntcolor,nlcolor,narad,nbrad,nlrad,ntfill
are # of types each array holds
actual length is nacolor+1 so that array can be indexed by 1-Ntype
setcolors() = set atom/bond/tri/line colors
setradii() = set atom/bond/line radii/thickness
setfill() = set triangle fill factor
extend() = grow an array
"""
# --------------------------------------------------------------------
def
__init__
(
self
):
self
.
acolor
=
[]
self
.
arad
=
[]
self
.
bcolor
=
[]
self
.
brad
=
[]
self
.
tcolor
=
[]
self
.
tfill
=
[]
self
.
lcolor
=
[]
self
.
lrad
=
[]
self
.
nacolor
=
self
.
narad
=
0
self
.
nbcolor
=
self
.
nbrad
=
0
self
.
ntcolor
=
self
.
ntfill
=
0
self
.
nlcolor
=
self
.
nlrad
=
0
# --------------------------------------------------------------------
# set color RGB for which = atoms, bonds, triangles
def
setcolors
(
self
,
which
,
ids
,
rgbs
):
# convert args into lists if single values
# if arg = 0, convert to full-range list
if
type
(
ids
)
is
types
.
IntType
and
ids
==
0
:
if
which
==
"atom"
:
ids
=
range
(
self
.
nacolor
)
if
which
==
"bond"
:
ids
=
range
(
self
.
nbcolor
)
if
which
==
"tri"
:
ids
=
range
(
self
.
ntcolor
)
if
which
==
"line"
:
ids
=
range
(
self
.
nlcolor
)
if
type
(
ids
)
is
not
types
.
ListType
and
type
(
ids
)
is
not
types
.
TupleType
:
ids
=
[
ids
]
if
type
(
rgbs
)
is
not
types
.
ListType
and
type
(
rgbs
)
is
not
types
.
TupleType
:
rgbs
=
[
rgbs
]
# if list of types has a 0, increment each type value
if
0
in
ids
:
for
i
in
xrange
(
len
(
ids
)):
ids
[
i
]
+=
1
# extend storage list if necessary
# extend other arrays for same "which" so that gl::make_atom_calllist
# has valid arrays to work with
if
which
==
"atom"
:
if
max
(
ids
)
>
self
.
nacolor
:
self
.
nacolor
=
self
.
extend
(
self
.
acolor
,
max
(
ids
))
self
.
nacolor
=
self
.
extend
(
self
.
arad
,
max
(
ids
))
if
which
==
"bond"
:
if
max
(
ids
)
>
self
.
nbcolor
:
self
.
nbcolor
=
self
.
extend
(
self
.
bcolor
,
max
(
ids
))
self
.
nbcolor
=
self
.
extend
(
self
.
brad
,
max
(
ids
))
if
which
==
"tri"
:
if
max
(
ids
)
>
self
.
ntcolor
:
self
.
ntcolor
=
self
.
extend
(
self
.
tcolor
,
max
(
ids
))
self
.
ntcolor
=
self
.
extend
(
self
.
tfill
,
max
(
ids
))
if
which
==
"line"
:
if
max
(
ids
)
>
self
.
nlcolor
:
self
.
nlcolor
=
self
.
extend
(
self
.
lcolor
,
max
(
ids
))
self
.
nlcolor
=
self
.
extend
(
self
.
lrad
,
max
(
ids
))
# set color for each type
# if list lengths match, set directly, else interpolate
# convert final color from 0-255 to 0.0-1.0
ntypes
=
len
(
ids
)
nrgbs
=
len
(
rgbs
)
for
i
in
xrange
(
ntypes
):
id
=
ids
[
i
]
if
rgbs
[
0
]
==
"loop"
:
list
=
colors
.
keys
()
red
,
green
,
blue
=
colors
[
list
[
i
%
len
(
colors
)]]
elif
ntypes
==
nrgbs
:
red
,
green
,
blue
=
colors
[
rgbs
[
i
]]
else
:
r
=
i
/
float
(
ntypes
-
1
)
*
float
(
nrgbs
-
1
)
jlo
=
int
(
r
)
jhi
=
jlo
+
1
if
jhi
==
nrgbs
:
jhi
=
nrgbs
-
1
clo
=
colors
[
rgbs
[
jlo
]]
chi
=
colors
[
rgbs
[
jhi
]]
delta
=
r
-
jlo
red
=
clo
[
0
]
+
delta
*
(
chi
[
0
]
-
clo
[
0
])
green
=
clo
[
1
]
+
delta
*
(
chi
[
1
]
-
clo
[
1
])
blue
=
clo
[
2
]
+
delta
*
(
chi
[
2
]
-
clo
[
2
])
color
=
[
red
/
255.0
,
green
/
255.0
,
blue
/
255.0
]
if
which
==
"atom"
:
self
.
acolor
[
id
]
=
color
if
which
==
"bond"
:
self
.
bcolor
[
id
]
=
color
if
which
==
"tri"
:
self
.
tcolor
[
id
]
=
color
if
which
==
"line"
:
self
.
lcolor
[
id
]
=
color
# --------------------------------------------------------------------
# set radii for which = atoms, bonds, lines
def
setradii
(
self
,
which
,
ids
,
radii
):
# convert args into lists if single values
# if arg = 0, convert to full-range list
if
type
(
ids
)
is
types
.
IntType
and
ids
==
0
:
if
which
==
"atom"
:
ids
=
range
(
self
.
narad
)
if
which
==
"bond"
:
ids
=
range
(
self
.
nbrad
)
if
which
==
"line"
:
ids
=
range
(
self
.
nlrad
)
if
type
(
ids
)
is
not
types
.
ListType
and
type
(
ids
)
is
not
types
.
TupleType
:
ids
=
[
ids
]
if
type
(
radii
)
is
not
types
.
ListType
and
\
type
(
radii
)
is
not
types
.
TupleType
:
radii
=
[
radii
]
# if list of types has a 0, increment each type value
if
0
in
ids
:
for
i
in
xrange
(
len
(
ids
)):
ids
[
i
]
+=
1
# extend storage list if necessary
# extend other arrays for same "which" so that gl::make_atom_calllist
# has valid arrays to work with
if
which
==
"atom"
:
if
max
(
ids
)
>
self
.
narad
:
self
.
narad
=
self
.
extend
(
self
.
arad
,
max
(
ids
))
self
.
narad
=
self
.
extend
(
self
.
acolor
,
max
(
ids
))
if
which
==
"bond"
:
if
max
(
ids
)
>
self
.
nbrad
:
self
.
nbrad
=
self
.
extend
(
self
.
brad
,
max
(
ids
))
self
.
nbrad
=
self
.
extend
(
self
.
bcolor
,
max
(
ids
))
if
which
==
"line"
:
if
max
(
ids
)
>
self
.
nlrad
:
self
.
nlrad
=
self
.
extend
(
self
.
lrad
,
max
(
ids
))
self
.
nlrad
=
self
.
extend
(
self
.
lcolor
,
max
(
ids
))
# set radius for each type
# if list lengths match, set directly, else interpolate
ntypes
=
len
(
ids
)
nradii
=
len
(
radii
)
for
i
in
range
(
ntypes
):
id
=
ids
[
i
]
if
ntypes
==
nradii
:
rad
=
radii
[
i
]
else
:
r
=
i
/
float
(
ntypes
-
1
)
*
float
(
nradii
-
1
)
jlo
=
int
(
r
)
jhi
=
jlo
+
1
if
jhi
==
nradii
:
jhi
=
nradii
-
1
rlo
=
radii
[
jlo
]
rhi
=
radii
[
jhi
]
delta
=
r
-
jlo
rad
=
rlo
+
delta
*
(
rhi
-
rlo
)
if
which
==
"atom"
:
self
.
arad
[
id
]
=
rad
if
which
==
"bond"
:
self
.
brad
[
id
]
=
rad
if
which
==
"line"
:
self
.
lrad
[
id
]
=
rad
# --------------------------------------------------------------------
# set triangle fill style
# 0 = fill only, 1 = line only, 2 = fill and line
def
setfills
(
self
,
which
,
ids
,
fills
):
# convert args into lists if single values
# if arg = 0, convert to full-range list
if
type
(
ids
)
is
types
.
IntType
and
ids
==
0
:
ids
=
range
(
self
.
ntfill
)
if
type
(
ids
)
is
not
types
.
ListType
and
type
(
ids
)
is
not
types
.
TupleType
:
ids
=
[
ids
]
if
type
(
fills
)
is
not
types
.
ListType
and
\
type
(
fills
)
is
not
types
.
TupleType
:
fills
=
[
fills
]
# if list of types has a 0, increment each type value
if
0
in
ids
:
for
i
in
xrange
(
len
(
ids
)):
ids
[
i
]
+=
1
# extend storage list if necessary
# extend other arrays for same "which" so that gl::make_atom_calllist
# has valid arrays to work with
if
max
(
ids
)
>
self
.
ntfill
:
self
.
ntfill
=
self
.
extend
(
self
.
tfill
,
max
(
ids
))
self
.
ntfill
=
self
.
extend
(
self
.
tcolor
,
max
(
ids
))
# set fill flag for each type
# if list lengths match, set directly, else set types to 1st fill value
if
len
(
fills
)
==
len
(
ids
):
for
i
in
xrange
(
len
(
ids
)):
self
.
tfill
[
ids
[
i
]]
=
int
(
fills
[
i
])
else
:
for
id
in
ids
:
self
.
tfill
[
id
]
=
int
(
fills
[
0
])
# --------------------------------------------------------------------
def
extend
(
self
,
array
,
n
):
for
i
in
range
(
n
-
len
(
array
)
+
1
):
array
.
append
(
0
)
return
n
# --------------------------------------------------------------------
# dictionary of 140 color names and associated RGB values
colors
=
{}
colors
[
"aliceblue"
]
=
[
240
,
248
,
255
]
colors
[
"antiquewhite"
]
=
[
250
,
235
,
215
]
colors
[
"aqua"
]
=
[
0
,
255
,
255
]
colors
[
"aquamarine"
]
=
[
127
,
255
,
212
]
colors
[
"azure"
]
=
[
240
,
255
,
255
]
colors
[
"beige"
]
=
[
245
,
245
,
220
]
colors
[
"bisque"
]
=
[
255
,
228
,
196
]
colors
[
"black"
]
=
[
0
,
0
,
0
]
colors
[
"blanchedalmond"
]
=
[
255
,
255
,
205
]
colors
[
"blue"
]
=
[
0
,
0
,
255
]
colors
[
"blueviolet"
]
=
[
138
,
43
,
226
]
colors
[
"brown"
]
=
[
165
,
42
,
42
]
colors
[
"burlywood"
]
=
[
222
,
184
,
135
]
colors
[
"cadetblue"
]
=
[
95
,
158
,
160
]
colors
[
"chartreuse"
]
=
[
127
,
255
,
0
]
colors
[
"chocolate"
]
=
[
210
,
105
,
30
]
colors
[
"coral"
]
=
[
255
,
127
,
80
]
colors
[
"cornflowerblue"
]
=
[
100
,
149
,
237
]
colors
[
"cornsilk"
]
=
[
255
,
248
,
220
]
colors
[
"crimson"
]
=
[
220
,
20
,
60
]
colors
[
"cyan"
]
=
[
0
,
255
,
255
]
colors
[
"darkblue"
]
=
[
0
,
0
,
139
]
colors
[
"darkcyan"
]
=
[
0
,
139
,
139
]
colors
[
"darkgoldenrod"
]
=
[
184
,
134
,
11
]
colors
[
"darkgray"
]
=
[
169
,
169
,
169
]
colors
[
"darkgreen"
]
=
[
0
,
100
,
0
]
colors
[
"darkkhaki"
]
=
[
189
,
183
,
107
]
colors
[
"darkmagenta"
]
=
[
139
,
0
,
139
]
colors
[
"darkolivegreen"
]
=
[
85
,
107
,
47
]
colors
[
"darkorange"
]
=
[
255
,
140
,
0
]
colors
[
"darkorchid"
]
=
[
153
,
50
,
204
]
colors
[
"darkred"
]
=
[
139
,
0
,
0
]
colors
[
"darksalmon"
]
=
[
233
,
150
,
122
]
colors
[
"darkseagreen"
]
=
[
143
,
188
,
143
]
colors
[
"darkslateblue"
]
=
[
72
,
61
,
139
]
colors
[
"darkslategray"
]
=
[
47
,
79
,
79
]
colors
[
"darkturquoise"
]
=
[
0
,
206
,
209
]
colors
[
"darkviolet"
]
=
[
148
,
0
,
211
]
colors
[
"deeppink"
]
=
[
255
,
20
,
147
]
colors
[
"deepskyblue"
]
=
[
0
,
191
,
255
]
colors
[
"dimgray"
]
=
[
105
,
105
,
105
]
colors
[
"dodgerblue"
]
=
[
30
,
144
,
255
]
colors
[
"firebrick"
]
=
[
178
,
34
,
34
]
colors
[
"floralwhite"
]
=
[
255
,
250
,
240
]
colors
[
"forestgreen"
]
=
[
34
,
139
,
34
]
colors
[
"fuchsia"
]
=
[
255
,
0
,
255
]
colors
[
"gainsboro"
]
=
[
220
,
220
,
220
]
colors
[
"ghostwhite"
]
=
[
248
,
248
,
255
]
colors
[
"gold"
]
=
[
255
,
215
,
0
]
colors
[
"goldenrod"
]
=
[
218
,
165
,
32
]
colors
[
"gray"
]
=
[
128
,
128
,
128
]
colors
[
"green"
]
=
[
0
,
128
,
0
]
colors
[
"greenyellow"
]
=
[
173
,
255
,
47
]
colors
[
"honeydew"
]
=
[
240
,
255
,
240
]
colors
[
"hotpink"
]
=
[
255
,
105
,
180
]
colors
[
"indianred"
]
=
[
205
,
92
,
92
]
colors
[
"indigo"
]
=
[
75
,
0
,
130
]
colors
[
"ivory"
]
=
[
255
,
240
,
240
]
colors
[
"khaki"
]
=
[
240
,
230
,
140
]
colors
[
"lavender"
]
=
[
230
,
230
,
250
]
colors
[
"lavenderblush"
]
=
[
255
,
240
,
245
]
colors
[
"lawngreen"
]
=
[
124
,
252
,
0
]
colors
[
"lemonchiffon"
]
=
[
255
,
250
,
205
]
colors
[
"lightblue"
]
=
[
173
,
216
,
230
]
colors
[
"lightcoral"
]
=
[
240
,
128
,
128
]
colors
[
"lightcyan"
]
=
[
224
,
255
,
255
]
colors
[
"lightgoldenrodyellow"
]
=
[
250
,
250
,
210
]
colors
[
"lightgreen"
]
=
[
144
,
238
,
144
]
colors
[
"lightgrey"
]
=
[
211
,
211
,
211
]
colors
[
"lightpink"
]
=
[
255
,
182
,
193
]
colors
[
"lightsalmon"
]
=
[
255
,
160
,
122
]
colors
[
"lightseagreen"
]
=
[
32
,
178
,
170
]
colors
[
"lightskyblue"
]
=
[
135
,
206
,
250
]
colors
[
"lightslategray"
]
=
[
119
,
136
,
153
]
colors
[
"lightsteelblue"
]
=
[
176
,
196
,
222
]
colors
[
"lightyellow"
]
=
[
255
,
255
,
224
]
colors
[
"lime"
]
=
[
0
,
255
,
0
]
colors
[
"limegreen"
]
=
[
50
,
205
,
50
]
colors
[
"linen"
]
=
[
250
,
240
,
230
]
colors
[
"magenta"
]
=
[
255
,
0
,
255
]
colors
[
"maroon"
]
=
[
128
,
0
,
0
]
colors
[
"mediumaquamarine"
]
=
[
102
,
205
,
170
]
colors
[
"mediumblue"
]
=
[
0
,
0
,
205
]
colors
[
"mediumorchid"
]
=
[
186
,
85
,
211
]
colors
[
"mediumpurple"
]
=
[
147
,
112
,
219
]
colors
[
"mediumseagreen"
]
=
[
60
,
179
,
113
]
colors
[
"mediumslateblue"
]
=
[
123
,
104
,
238
]
colors
[
"mediumspringgreen"
]
=
[
0
,
250
,
154
]
colors
[
"mediumturquoise"
]
=
[
72
,
209
,
204
]
colors
[
"mediumvioletred"
]
=
[
199
,
21
,
133
]
colors
[
"midnightblue"
]
=
[
25
,
25
,
112
]
colors
[
"mintcream"
]
=
[
245
,
255
,
250
]
colors
[
"mistyrose"
]
=
[
255
,
228
,
225
]
colors
[
"moccasin"
]
=
[
255
,
228
,
181
]
colors
[
"navajowhite"
]
=
[
255
,
222
,
173
]
colors
[
"navy"
]
=
[
0
,
0
,
128
]
colors
[
"oldlace"
]
=
[
253
,
245
,
230
]
colors
[
"olive"
]
=
[
128
,
128
,
0
]
colors
[
"olivedrab"
]
=
[
107
,
142
,
35
]
colors
[
"orange"
]
=
[
255
,
165
,
0
]
colors
[
"orangered"
]
=
[
255
,
69
,
0
]
colors
[
"orchid"
]
=
[
218
,
112
,
214
]
colors
[
"palegoldenrod"
]
=
[
238
,
232
,
170
]
colors
[
"palegreen"
]
=
[
152
,
251
,
152
]
colors
[
"paleturquoise"
]
=
[
175
,
238
,
238
]
colors
[
"palevioletred"
]
=
[
219
,
112
,
147
]
colors
[
"papayawhip"
]
=
[
255
,
239
,
213
]
colors
[
"peachpuff"
]
=
[
255
,
239
,
213
]
colors
[
"peru"
]
=
[
205
,
133
,
63
]
colors
[
"pink"
]
=
[
255
,
192
,
203
]
colors
[
"plum"
]
=
[
221
,
160
,
221
]
colors
[
"powderblue"
]
=
[
176
,
224
,
230
]
colors
[
"purple"
]
=
[
128
,
0
,
128
]
colors
[
"red"
]
=
[
255
,
0
,
0
]
colors
[
"rosybrown"
]
=
[
188
,
143
,
143
]
colors
[
"royalblue"
]
=
[
65
,
105
,
225
]
colors
[
"saddlebrown"
]
=
[
139
,
69
,
19
]
colors
[
"salmon"
]
=
[
250
,
128
,
114
]
colors
[
"sandybrown"
]
=
[
244
,
164
,
96
]
colors
[
"seagreen"
]
=
[
46
,
139
,
87
]
colors
[
"seashell"
]
=
[
255
,
245
,
238
]
colors
[
"sienna"
]
=
[
160
,
82
,
45
]
colors
[
"silver"
]
=
[
192
,
192
,
192
]
colors
[
"skyblue"
]
=
[
135
,
206
,
235
]
colors
[
"slateblue"
]
=
[
106
,
90
,
205
]
colors
[
"slategray"
]
=
[
112
,
128
,
144
]
colors
[
"snow"
]
=
[
255
,
250
,
250
]
colors
[
"springgreen"
]
=
[
0
,
255
,
127
]
colors
[
"steelblue"
]
=
[
70
,
130
,
180
]
colors
[
"tan"
]
=
[
210
,
180
,
140
]
colors
[
"teal"
]
=
[
0
,
128
,
128
]
colors
[
"thistle"
]
=
[
216
,
191
,
216
]
colors
[
"tomato"
]
=
[
253
,
99
,
71
]
colors
[
"turquoise"
]
=
[
64
,
224
,
208
]
colors
[
"violet"
]
=
[
238
,
130
,
238
]
colors
[
"wheat"
]
=
[
245
,
222
,
179
]
colors
[
"white"
]
=
[
255
,
255
,
255
]
colors
[
"whitesmoke"
]
=
[
245
,
245
,
245
]
colors
[
"yellow"
]
=
[
255
,
255
,
0
]
colors
[
"yellowgreen"
]
=
[
154
,
205
,
50
]
Event Timeline
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