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10 from tempfile import mktemp
11 import os
12 from MMTK import Units
13
14
15 template = {'REF' : {}, 'NEW' : {}}
16
17 template['REF']['title'] = 'Incoherent Scattering Function'
18 template['REF']['log_file'] = 'logfile.log'
19 template['REF']['output_files'] = {'fft' : 'DISF_Sqw_test.nc', 'isf' : 'DISF_Fqt_test.nc'}
20 template['REF']['units_frequency'] = 1/Units.ps
21 template['REF']['trajectory'] = ['../TrajectoryTest1.nc']
22 template['REF']['weights'] = 'incoherent'
23 template['REF']['units_q'] = 1/Units.nm
24 template['REF']['frequency_points'] = 1000000
25
26
27 template['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc')
28 template['NEW']['weights'] = 'incoherent'
29 template['NEW']['disf'] = mktemp(suffix = '_ISF.nc', prefix = 'nMOLDYN_')
30 template['NEW']['qVectorsGenerator'] = "3d isotropic"
31 template['NEW']['qVectorsDirection'] = None
32 template['NEW']['qVectorsPerShell'] = 500
33 template['NEW']['pyroserver'] = 'monoprocessor'
34 template['NEW']['analysis'] = 'DynamicIncoherentStructureFactor_serial(self.testParameters)'
35
36 test = []
37
38
39 test.append({'REF' : {}, 'NEW' : {}})
40
41 test[-1]['REF']['time_info'] = (0, 49, 1)
42 test[-1]['REF']['atoms_pdb'] = '../TrajectoryTest1_1.pdb'
43 test[-1]['REF']['deuter'] = None
44 test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0], 1.000000, 500, None)
45 test[-1]['REF']['ft_window'] = 80.0
46
47
48 test[-1]['NEW']['timeinfo'] = '1:49:1'
49 test[-1]['NEW']['subset'] = 'filename %s' % os.path.join(nmoldyn_package_path,"Tests",'TrajectoryTest1_1.nms')
50 test[-1]['NEW']['deuteration'] = None
51 test[-1]['NEW']['qShellValues'] = "3.:10.:1."
52 test[-1]['NEW']['qShellWidth'] = 1.0
53 test[-1]['NEW']['fftWindow'] = 100./80.0
54
55
56
57 test.append({'REF' : {}, 'NEW' : {}})
58
59 test[-1]['REF']['time_info'] = (0, 19, 1)
60 test[-1]['REF']['atoms'] = {'Protein.0': ["BackBone"]}
61 test[-1]['REF']['deuter'] = None
62 test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0], 0.800000, 500, None)
63 test[-1]['REF']['ft_window'] = 10.0
64
65
66 test[-1]['NEW']['timeinfo'] = '1:19:1'
67 test[-1]['NEW']['subset'] = 'objectname P892 misc backbone'
68 test[-1]['NEW']['deuteration'] = None
69 test[-1]['NEW']['qShellValues'] = "3.:10.:1.0"
70 test[-1]['NEW']['qShellWidth'] = 0.8
71 test[-1]['NEW']['fftWindow'] = 100./10.0
72
73
74
75 test.append({'REF' : {}, 'NEW' : {}})
76
77 test[-1]['REF']['time_info'] = (0, 19, 2)
78 test[-1]['REF']['atoms'] = {'Protein.0': ['Methyl']}
79 test[-1]['REF']['deuter'] = None
80 test[-1]['REF']['q_vector_set'] = ([3.0, 5.0, 7.0, 9.0], 0.800000, 500, None)
81 test[-1]['REF']['ft_window'] = 20.0
82
83
84 test[-1]['NEW']['timeinfo'] = '1:19:2'
85 test[-1]['NEW']['subset'] = 'objectname P892 chemfragment methyl'
86 test[-1]['NEW']['deuteration'] = None
87 test[-1]['NEW']['qShellValues'] = "3.:9.:2.0"
88 test[-1]['NEW']['qShellWidth'] = 0.8
89 test[-1]['NEW']['fftWindow'] = 100./20.0
90
91
92
93 test.append({'REF' : {}, 'NEW' : {}})
94
95 test[-1]['REF']['time_info'] = (0, 9, 1)
96 test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen','Nitrogen']}
97 test[-1]['REF']['deuter'] = None
98 test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0], 1.200000, 500, None)
99 test[-1]['REF']['ft_window'] = 50.0
100
101
102 test[-1]['NEW']['timeinfo'] = '1:9:1'
103 test[-1]['NEW']['subset'] = 'objectname P892 atomelement nitrogen,oxygen'
104 test[-1]['NEW']['deuteration'] = None
105 test[-1]['NEW']['qShellValues'] = "4.:8.:1.0"
106 test[-1]['NEW']['qShellWidth'] = 1.2
107 test[-1]['NEW']['fftWindow'] = 100./50.0
108
109
110
111 test.append({'REF' : {}, 'NEW' : {}})
112
113 test[-1]['REF']['time_info'] = (5, 29, 3)
114 test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']}
115 test[-1]['REF']['deuter'] = None
116 test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0, 9.0], 0.900000, 500, None)
117 test[-1]['REF']['ft_window'] = 10.0
118
119
120 test[-1]['NEW']['timeinfo'] = '6:29:3'
121 test[-1]['NEW']['subset'] = 'objectname P892 atomelement hydrogen'
122 test[-1]['NEW']['deuteration'] = None
123 test[-1]['NEW']['qShellValues'] = "4.:9.:1.0"
124 test[-1]['NEW']['qShellWidth'] = 0.9
125 test[-1]['NEW']['fftWindow'] = 100./10.0
126
127
128
129 test.append({'REF' : {}, 'NEW' : {}})
130
131 test[-1]['REF']['time_info'] = (4, 23, 2)
132 test[-1]['REF']['atoms'] = {'Protein.0': ['*']}
133 test[-1]['REF']['deuter'] = {'Protein.0': ['Methyl']}
134 test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 6.0, 7.0, 9.0], 1.00000, 500, None)
135 test[-1]['REF']['ft_window'] = 40.0
136
137
138 test[-1]['NEW']['timeinfo'] = '5:23:2'
139 test[-1]['NEW']['subset'] = None
140 test[-1]['NEW']['deuteration'] = 'objectname P892 chemfragment methyl'
141 test[-1]['NEW']['qShellValues'] = [3.0, 4.0, 6.0, 7.0, 9.0]
142 test[-1]['NEW']['qShellWidth'] = 1.0
143 test[-1]['NEW']['fftWindow'] = 100./40.0
144
145
146
147 test.append({'REF' : {}, 'NEW' : {}})
148
149 test[-1]['REF']['time_info'] = (0, 19, 1)
150 test[-1]['REF']['atoms'] = {'Protein.0': ['Carbon']}
151 test[-1]['REF']['deuter'] = None
152 test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0], 0.500000, 500, None)
153 test[-1]['REF']['ft_window'] = 80.0
154
155
156 test[-1]['NEW']['timeinfo'] = '1:19:1'
157 test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon'
158 test[-1]['NEW']['deuteration'] = None
159 test[-1]['NEW']['qShellValues'] = "4.:8.:1.0"
160 test[-1]['NEW']['qShellWidth'] = 0.5
161 test[-1]['NEW']['fftWindow'] = 100./80.0
162
163
164
165 test.append({'REF' : {}, 'NEW' : {}})
166
167 test[-1]['REF']['time_info'] = (3, 39, 4)
168 test[-1]['REF']['atoms'] = {'Protein.0': ['Sulfur']}
169 test[-1]['REF']['deuter'] = None
170 test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0], 1.800000, 500, None)
171 test[-1]['REF']['ft_window'] = 10.0
172
173
174 test[-1]['NEW']['timeinfo'] = '4:39:4'
175 test[-1]['NEW']['subset'] = 'objectname P892 atomelement sulfur'
176 test[-1]['NEW']['deuteration'] = None
177 test[-1]['NEW']['qShellValues'] = "3.:6.:1.0"
178 test[-1]['NEW']['qShellWidth'] = 1.8
179 test[-1]['NEW']['fftWindow'] = 100./10.0
180
181
182
183 test.append({'REF' : {}, 'NEW' : {}})
184
185 test[-1]['REF']['time_info'] = (0, 19, 1)
186 test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
187 test[-1]['REF']['deuter'] = {'Protein.0': ['Hydrogen']}
188 test[-1]['REF']['q_vector_set'] = ([7.5, 8.5, 9.5], 0.800000, 500, None)
189 test[-1]['REF']['ft_window'] = 20.0
190
191
192 test[-1]['NEW']['timeinfo'] = '1:19:1'
193 test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
194 test[-1]['NEW']['deuteration'] = 'objectname P892 atomelement hydrogen'
195 test[-1]['NEW']['qShellValues'] = "7.5:9.5:1.0"
196 test[-1]['NEW']['qShellWidth'] = 0.8
197 test[-1]['NEW']['fftWindow'] = 100./20.0
198
199
200
201 test.append({'REF' : {}, 'NEW' : {}})
202
203 test[-1]['REF']['time_info'] = (3, 30, 3)
204 test[-1]['REF']['atoms'] = {'Protein.0': ['BackBone','SideChain']}
205 test[-1]['REF']['deuter'] = None
206 test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0, 7.0], 1.500000, 500, None)
207 test[-1]['REF']['ft_window'] = 25.0
208
209
210 test[-1]['NEW']['timeinfo'] = '4:30:3'
211 test[-1]['NEW']['subset'] = 'objectname P892 misc backbone,sidechains'
212 test[-1]['NEW']['deuteration'] = None
213 test[-1]['NEW']['qShellValues'] = "3.:7.:1.0"
214 test[-1]['NEW']['qShellWidth'] = 1.5
215 test[-1]['NEW']['fftWindow'] = 100./25.0
216
217
218
219 test.append({'REF' : {}, 'NEW' : {}})
220
221 test[-1]['REF']['time_info'] = (5, 19, 2)
222 test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']}
223 test[-1]['REF']['deuter'] = None
224 test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0], 1.000000, 500, None)
225 test[-1]['REF']['ft_window'] = 10.0
226
227
228 test[-1]['NEW']['timeinfo'] = '6:19:2'
229 test[-1]['NEW']['subset'] = 'objectname P892 atomelement hydrogen'
230 test[-1]['NEW']['deuteration'] = None
231 test[-1]['NEW']['qShellValues'] = "3.:10.:1.0"
232 test[-1]['NEW']['qShellWidth'] = 1.0
233 test[-1]['NEW']['fftWindow'] = 100./10.0
234
235
236
237 test.append({'REF' : {}, 'NEW' : {}})
238
239 test[-1]['REF']['time_info'] = (0, 19, 1)
240 test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen', 'Nitrogen', 'Carbon', 'Sulfur', 'Hydrogen']}
241 test[-1]['REF']['deuter'] = None
242 test[-1]['REF']['q_vector_set'] = ([3.2, 4.2, 5.6, 6.4, 7.3], 0.600000, 500, None)
243 test[-1]['REF']['ft_window'] = 8.0
244
245
246 test[-1]['NEW']['timeinfo'] = '1:19:1'
247 test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon,hydrogen,nitrogen,oxygen,sulfur'
248 test[-1]['NEW']['deuteration'] = None
249 test[-1]['NEW']['qShellValues'] = (3.2, 4.2, 5.6, 6.4, 7.3)
250 test[-1]['NEW']['qShellWidth'] = 0.6
251 test[-1]['NEW']['fftWindow'] = 100./8.0
252