source: ThirdParty/mpqc_open/src/lib/chemistry/molecule/moltest.in@ 7516f6

Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
Last change on this file since 7516f6 was 860145, checked in by Frederik Heber <heber@…>, 8 years ago

Merge commit '0b990dfaa8c6007a996d030163a25f7f5fc8a7e7' as 'ThirdParty/mpqc_open'
  • Property mode set to 100644
File size: 11.9 KB
Line 
1% Emacs should use -*- keyval -*- mode.
2
3atominfo<AtomInfo>: (
4 vdw_radius: (
5 scale_factor = 1.2
6 unit = angstrom
7 H = 1.3
8 Li = 0.1818
9 )
10 bragg_radius: (
11 unit = angstrom
12 H = 0.888
13 )
14 atomic_radius: (
15 unit = angstrom
16 H = 0.999
17 )
18 rgb: (
19 H = [ 0.0 0.0 1.0 ]
20 He:2 = 0.5
21 )
22 mass: (
23 unit = amu
24 H = 2.1
25 )
26 )
27
28energy<TaylorMolecularEnergy>: (
29 molecule<Molecule>: (
30 symmetry = c2v
31 { atom_labels atoms geometry } = {
32 O O [0.0 0.0 0.0]
33 H1 H [0.0 1.0 1.0]
34 H2 H [0.0 -1.0 1.0]
35 }
36 )
37 coordinates<SetIntCoor>: [
38 <StreSimpleCo>: ( atoms = [ 1 2 ] label = "r(OH1)" )
39 <StreSimpleCo>: ( atoms = [ 1 3 ] label = "r(OH2)" )
40 <BendSimpleCo>: ( atoms = [ 2 1 3 ] label = "theta(HOH)" )
41 ]
42% force_constants: [
43% [ 1 1 4.0 ]
44% [ 2 2 4.0 ]
45% [ 3 3 2.0 ]
46% [ 1 2 1.5 ]
47% [ 1 3 0.5 ]
48% [ 2 3 0.5 ]
49% ]
50 )
51
52% TaylorMolecularEnergy does work with FinDispMolecularHessian
53xhess<FinDispMolecularHessian>: (
54 energy = $:energy
55 )
56
57freq<MolecularFrequencies>: (
58 molecule = $:molecule
59 )
60
61big_molecule<Molecule>: (
62 angstrom = yes
63 %symmetry=d2h
64 %redundant_atoms=yes
65 xsymmetry_frame = [
66 [ 1 0 0 ]
67 [ 0 0 1 ]
68 [ 0 1 0 ]
69 ]
70
71 { atoms geometry } =
72 {
73 n [ 0.000000 0.000000 0.000000 ]
74 c [ 0.000000 0.000000 1.340853 ]
75 c [ 1.276285 0.000000 -0.411067 ]
76 n [ -1.044424 0.000000 2.149457 ]
77 n [ 1.725764 0.000000 -1.653098 ]
78 c [ 1.370758 0.000000 1.856359 ]
79 c [ 2.187205 0.000000 0.735648 ]
80 c [ 1.901357 0.000000 3.136948 ]
81 c [ 3.568793 0.000000 0.848106 ]
82 c [ -2.281309 0.000000 1.747151 ]
83 c [ 0.963636 0.000000 -2.707089 ]
84 n [ -0.394169 0.000000 -2.765670 ]
85 c [ 3.278826 0.000000 3.254057 ]
86 c [ 4.102557 0.000000 2.123344 ]
87 c [ -3.446446 0.000000 2.607232 ]
88 c [ 1.425101 0.000000 -4.079798 ]
89 h [ 1.264025 0.000000 4.001762 ]
90 h [ 4.196577 0.000000 -0.023664 ]
91 n [ -2.753333 0.000000 0.472687 ]
92 h [ -2.168546 0.000000 -0.330035 ]
93 h [ -0.978957 0.000000 -1.962948 ]
94 c [ -4.111141 0.000000 0.414104 ]
95 c [ -0.866194 0.000000 -4.040136 ]
96 c [ -4.572607 0.000000 1.786813 ]
97 c [ 0.298944 0.000000 -4.900217 ]
98 c [ -3.566512 0.000000 3.996510 ]
99 c [ 2.710672 0.000000 -4.619997 ]
100 c [ 5.428715 0.000000 2.285234 ]
101 c [ 3.839479 0.000000 4.466728 ]
102 n [ -4.873266 0.000000 -0.639886 ]
103 n [ -2.103077 0.000000 -4.442443 ]
104 c [ -5.858176 0.000000 2.327010 ]
105 c [ 0.419010 0.000000 -6.289496 ]
106 c [ -4.834777 0.000000 4.525021 ]
107 c [ 2.824921 0.000000 -5.989220 ]
108 h [ -2.693531 0.000000 4.621985 ]
109 h [ 3.573663 0.000000 -3.980803 ]
110 c [ 5.952960 0.000000 3.517888 ]
111 h [ 6.074619 0.000000 1.391664 ]
112 c [ 5.173494 0.000000 4.587840 ]
113 h [ 3.186948 0.000000 5.355469 ]
114 c [ -4.423788 0.000000 -1.881917 ]
115 c [ -3.147503 0.000000 -3.633837 ]
116 c [ -5.972424 0.000000 3.696235 ]
117 c [ 1.687276 0.000000 -6.818005 ]
118 h [ -6.721165 0.000000 1.687817 ]
119 h [ -0.453971 0.000000 -6.914970 ]
120 h [ 7.044639 0.000000 3.672463 ]
121 h [ 5.655300 0.000000 5.579569 ]
122 c [ 4.036295 0.000000 -6.552673 ]
123 c [ -4.999726 0.000000 5.850803 ]
124 n [ -3.147503 0.000000 -2.292984 ]
125 c [ -5.334707 0.000000 -3.028633 ]
126 c [ -4.518262 0.000000 -4.149345 ]
127 c [ 4.154329 0.000000 -7.886964 ]
128 h [ 4.926541 0.000000 -5.902195 ]
129 c [ 1.852220 0.000000 -8.143787 ]
130 c [ -7.183797 0.000000 4.259686 ]
131 c [ -6.233581 0.000000 6.372209 ]
132 h [ -4.107647 0.000000 6.498765 ]
133 c [ -6.716298 0.000000 -3.141092 ]
134 c [ -5.048860 0.000000 -5.429932 ]
135 h [ 5.144938 0.000000 -8.371058 ]
136 c [ 3.086078 0.000000 -8.665193 ]
137 h [ 0.960144 0.000000 -8.791748 ]
138 c [ -7.301831 0.000000 5.593979 ]
139 h [ -8.074043 0.000000 3.609208 ]
140 h [ -6.390672 0.000000 7.463531 ]
141 c [ -7.250060 0.000000 -4.416331 ]
142 c [ -6.426328 0.000000 -5.547041 ]
143 h [ -7.344080 0.000000 -2.269320 ]
144 h [ -4.411528 0.000000 -6.294749 ]
145 h [ 3.243167 0.000000 -9.756515 ]
146 h [ -8.292441 0.000000 6.078073 ]
147 c [ -6.986981 0.000000 -6.759712 ]
148 c [ -8.576216 0.000000 -4.578218 ]
149 c [ -8.320998 0.000000 -6.880823 ]
150 h [ -6.334453 0.000000 -7.648453 ]
151 c [ -9.099795 0.000000 -5.811154 ]
152 h [ -9.222599 0.000000 -3.684999 ]
153 h [ -8.802806 0.000000 -7.872550 ]
154 h [ -10.191392 0.000000 -5.966319 ]
155 }
156 )
157
158small_molecule<Molecule>: (
159 angstrom = no
160 { atoms geometry } =
161 {
162 O [ 0.000000 0.000000 0.000000 ]
163 H [ 0.000000 1.000000 1.000000 ]
164 H [ 0.000000 -1.000000 1.000000 ]
165 }
166 )
167
168linear_molecule<Molecule>: (
169 angstrom = no
170 { atoms geometry } =
171 {
172 H [ 0.000000 0.100000 2.000000 ]
173 C [ 0.000000 0.000000 1.000000 ]
174 C [ 0.000000 0.000000 -1.000000 ]
175 H [ 0.000000 0.200000 -2.000000 ]
176 }
177 )
178
179enediyne<Molecule>: (
180 symmetry = C2V
181 angstroms = no
182 { atoms geometry } = {
183 H [ -5.3870492639 -0.0000000000 1.3995052531 ]
184 H [ 5.3870492639 -0.0000000000 1.3995052531 ]
185 C [ -4.1906139895 -0.0000000000 -0.2149062043 ]
186 C [ 4.1906139895 -0.0000000000 -0.2149062043 ]
187 C [ -2.8240829859 0.0000000000 -2.0097148495 ]
188 C [ 2.8240829859 -0.0000000000 -2.0097148495 ]
189 C [ -1.2579864521 -0.0000000000 -4.2267821010 ]
190 C [ 1.2579864521 0.0000000000 -4.2267821010 ]
191 H [ -2.2391693577 -0.0000000000 -6.0205520984 ]
192 H [ 2.2391693577 -0.0000000000 -6.0205520984 ]
193 }
194 atom_labels:1 = "H2"
195)
196
197molecule = $:small_molecule
198
199big_molcoor<SymmMolecularCoor>: (
200 molecule = $:big_molecule
201 scale_bonds = 16.0
202 scale_bends = 4.0
203 simple_tolerance = 0.05
204 update_bmatrix = yes
205 given_fixed_values = yes
206 fixed<SetIntCoor>: [
207 <StreSimpleCo>: ( atoms = [ 1 2 ] label = "r(OH)" value = 1.0 )
208 %<StreSimpleCo> = [ "r(OH)" 1 2 ]
209 %<BendSimpleCo> = [ "a(HOH)" 2 1 3 ]
210 ]
211 extra_bonds = [ 1 3 2 4 1 4 ]
212 )
213
214small_molcoor<SymmMolecularCoor>: (
215 molecule = $:small_molecule
216 scale_bonds = 16.0
217 scale_bends = 4.0
218 simple_tolerance = 0.05
219 update_bmatrix = yes
220 have_fixed_values = yes
221 max_update_steps = 100
222 max_update_disp = 100.0
223 fixed<SetIntCoor>: [
224 <StreSimpleCo>: ( atoms = [ 2 3 ] label = "r(HH)" value = 1.5 )
225 %<StreSimpleCo>: ( atoms = [ 1 3 ] label = "r(OH)" value = 2.2 )
226 ]
227 )
228
229small_redund_molcoor<RedundMolecularCoor>: (
230 molecule = $:small_molecule
231 )
232
233medium_molcoor<SymmMolecularCoor>: (
234 molecule<Molecule>: (
235 angstrom = yes
236 { atoms geometry } =
237 {
238 C [ -1.481978 1.137918 0.053920]
239 C [ -2.377552 -0.058848 0.015422]
240 N [ -0.256358 0.721189 0.007050]
241 H [ -1.754455 2.190795 0.079781]
242 C [ -0.326866 -0.730249 -0.014562]
243 C [ 1.043217 1.561636 -0.056035]
244 N [ -1.671068 -1.129599 -0.036351]
245 H [ -3.465237 -0.021159 0.023663]
246 H [ 1.063541 2.111989 0.901108]
247 H [ 0.887902 2.255657 -0.891111]
248 N [ 0.656762 -1.486673 0.005244]
249 H [ 2.056209 0.795245 -0.136829]
250 H [ 0.425921 -2.467905 -0.021317]
251 H [ 1.917997 -1.027989 0.094573]
252 O [ 2.866992 -0.212573 -0.043377]
253 H [ 3.685907 -0.333218 0.473075]
254 }
255 )
256 scale_bonds = 16.0
257 scale_bends = 4.0
258 simple_tolerance = 0.05
259 update_bmatrix = yes
260 max_update_steps = 200
261 max_update_disp = 0.5
262 have_fixed_values = yes
263 fixed<SetIntCoor>: [
264 <SumIntCoor>: (
265 unit = bohr
266 value = 0.1
267 label = "Reaction Coordinate"
268 coor: [
269 <StreSimpleCo>: (atoms = [ 6 12] label = "r(CH)")
270 <StreSimpleCo>: (atoms = [12 15] label = "r(HO)")
271 <StreSimpleCo>: (atoms = [15 14] label = "r(OH)")
272 <StreSimpleCo>: (atoms = [14 11] label = "r(HN)")
273 ]
274 coef = [
275 1.0
276 -1.0
277 1.0
278 -1.0
279 ]
280 )
281 ]
282 extra_bonds = [ 12 6 12 15 14 15 11 14 ]
283 )
284
285molcoor = $:small_redund_molcoor
286
287custom_simp<SetIntCoor>: [
288 <StreSimpleCo> = [ "st____1" 1 2 ]
289 <StreSimpleCo> = [ "st2" 1 3 ]
290 <SumIntCoor>: (
291 label = "lin1"
292 value = 1.1
293 { coef coor } = {
294 1.0 $:simp:0
295 -1.0 $:simp:1
296 }
297 )
298 <StreSimpleCo> = ["st2_again" 1 3]
299 <SumIntCoor>: (
300 label = "lin2"
301 value = 1.1
302 { coef coor } = {
303 1.0 $:simp:0
304 -1.0 $:simp:1
305 -1.0 $:simp:2
306 -1.0 $:simp:3
307 }
308 )
309 ]
310
311generator<IntCoorGen>: (
312 molecule = $:molecule
313 linear_bend = no
314 linear_bend_threshold = 10.0
315 linear_tors = no
316 linear_tors_threshold = 10.0
317 )
318
319generated_simp<SetIntCoor>: (
320 generator = $:generator
321 )
322
323simp = $:generated_simp
324
325bmat_test = $:simp
326
327renderer<OOGLRender>: (
328 filename = "moltest.oogl"
329 )
330
331ball<RenderedBallMolecule>: (
332 appearance<Appearance>: (
333 level = 3
334 )
335 molecule = $..:molecule
336 atominfo = $..:atominfo
337 )
338
339surf<RenderedMolecularSurface>: (
340 surface<TriangulatedImplicitSurface>: (
341 surface<TriangulatedSurface>: (
342 verbose = yes
343 )
344 vdw<VDWShape>: (
345 molecule = $:molecule
346 atominfo = $:atominfo
347 )
348 con<ConnollyShape>: (
349 molecule = $:molecule
350 probe_radius = 2.6456173
351 atominfo = $:atominfo
352 )
353 volume = $con
354 resolution = 0.5
355 remove_short_edges = 1
356 remove_slender_triangles = 1
357 short_edge_factor = 0.4
358 slender_triangle_factor = 0.2
359 initialize = yes
360 )
361 molecule = $:molecule
362 atominfo = $:atominfo
363 )
364
365renderedmolecule = $:surf
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