/
quickff.log
398 lines (286 loc) · 17.7 KB
/
quickff.log
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
________________/\\\_________/\\\\\\\\\\\\\\\__/\\\\\\\\\\\\\\\_________________
______________/\\\\/\\\\_____\/\\\///////////__\/\\\///////////_________________
_____________/\\\//\////\\\___\/\\\_____________\/\\\___________________________
_____________/\\\______\//\\\__\/\\\\\\\\\\\_____\/\\\\\\\\\\\__________________
_____________\//\\\______/\\\___\/\\\///////______\/\\\///////__________________
_______________\///\\\\/\\\\/____\/\\\_____________\/\\\________________________
__________________\////\\\//______\/\\\_____________\/\\\_______________________
______________________\///\\\\\\___\/\\\_____________\/\\\______________________
_________________________\//////____\///______________\///______________________
Welcom to QuickFF
a Python package to quickly derive force fields from ab initio input data
Written by
Louis Vanduyfhuys(1)*, Steven Vandenbrande(1) and Toon Verstraelen(1)
(1) Center for Molecular Modeling, Ghent University Belgium.
* mailto: Louis.Vanduyfhuys@UGent.be
USER vsc41947
MACHINE Linux gligar05.gastly.os 3.10.0-1062.9.1.el7.ug.x86_64 #1
MACHINE SMP Wed Jan 22 12:35:53 CET 2020 x86_64
TIME 2020-03-10 11:24:31.742507
QUICKFF VERSION 2.2.1
PYTHON VERSION 3.7.2 (default, Apr 9 2019, 14:23:44) [GCC 8.2.0]
NUMPY VERSION 1.16.2
SCIPY VERSION 1.2.1
MATPLOTLIB VERSION 3.0.3
CURRENT DIR /kyukon/scratch/gent/vo/000/gvo00003/vsc41947/pyiron/
CURRENT DIR projects/nanoscale/week11/benzene/ei_hdf5/ei
COMMAND LINE /data/gent/vo/000/gvo00003/vsc40312_apps/victini/software/
COMMAND LINE QuickFF/2.2.3-intel-2019a-Python-3.7.2/bin/qff.py -c
COMMAND LINE config.txt input.chk
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SETT bend_term BendAHarm
SETT bond_term BondHarm
SETT consistent_cross_rvs True
SETT covres None
SETT cross_svd_rcond 1e-08
SETT do_bendclin True
SETT do_bends True
SETT do_bonds True
SETT do_cross_ASA True
SETT do_cross_ASS True
SETT do_cross_DAA False
SETT do_cross_DAD False
SETT do_cross_DSD False
SETT do_cross_DSS False
SETT do_cross_svd True
SETT do_dihedrals True
SETT do_hess_mass_weighting True
SETT do_hess_negfreq_proj False
SETT do_oops True
SETT do_sqoopdist_to_oopdist True
SETT do_squarebend True
SETT ei pars_mbisgauss.txt
SETT ei_rcut None
SETT excl_bends None
SETT excl_bonds None
SETT excl_dihs None
SETT excl_oopds None
SETT ffatypes None
SETT fn_charmm22_prm None
SETT fn_charmm22_psf None
SETT fn_sys system.chk
SETT fn_traj None
SETT fn_yaff pars_cov.txt
SETT log_file quickff.log
SETT log_level high
SETT only_traj PT_ALL
SETT pert_traj_energy_noise None
SETT pert_traj_tol 0.001
SETT plot_traj None
SETT program_mode DeriveFF
SETT remove_dysfunctional_cross True
SETT vdw None
SETT vdw_rcut 37.79452267842504
SETT xyz_traj False
INIT Initializing system
INIT Initializing Second order taylor reference for ai
INIT Initializing Yaff force field reference for EI
INIT Initializing program
VAL Initializing valence force field
VAL Added 12 bond terms
VAL Added 18 bend terms (an)harmonic in the angle, 0 bend terms with
VAL 1+cos(angle) potential and 0 bend terms with 1-cos(4*theta) potential.
VAL Added 24 Cosine dihedral terms (of which 24 are described using
VAL Chebychev terms)
VAL Added 6 Harmonic and 0 SquareHarmonic out-of-plane distance terms
SYS Atomic configuration of the system:
SYS index | x [A] | y [A] | z [A] | ffatype | q | R [A]
SYS ---------------------------------------------------------------------
SYS 0 | 0.000 | 1.398 | -0.000 | C | -0.132 | 1.170
SYS 1 | 0.000 | 0.699 | 1.211 | C | -0.132 | 1.170
SYS 2 | -0.000 | -0.699 | 1.211 | C | -0.132 | 1.170
SYS 3 | -0.000 | -1.398 | -0.000 | C | -0.132 | 1.170
SYS 4 | 0.000 | -0.699 | -1.211 | C | -0.132 | 1.170
SYS 5 | 0.000 | 0.699 | -1.211 | C | -0.132 | 1.170
SYS 6 | 0.000 | 2.486 | 0.000 | H | 0.131 | 0.731
SYS 7 | -0.000 | 1.243 | 2.153 | H | 0.131 | 0.731
SYS 8 | -0.000 | -1.243 | 2.153 | H | 0.131 | 0.731
SYS 9 | -0.000 | -2.486 | 0.000 | H | 0.131 | 0.731
SYS 10 | 0.000 | -1.243 | -2.153 | H | 0.131 | 0.731
SYS 11 | 0.000 | 1.243 | -2.153 | H | 0.131 | 0.731
EQSET Resetting system coordinates to ab initio ref
EQSET Setting rest values to AI equilibrium values for tasks EQ_RV
BondHarm/C.C (kjmol/A^2 A)
fc = +- rv = +-
BondHarm/C.H (kjmol/A^2 A)
fc = +- rv = +-
BendAHarm/C.C.C (kjmol/rad^2 deg)
fc = +- rv = +-
BendAHarm/C.C.H (kjmol/rad^2 deg)
fc = +- rv = +-
TorsCheby2/C.C.C.C (kjmol au)
fc = +- sgn = -1
TorsCheby2/C.C.C.H (kjmol au)
fc = +- sgn = -1
TorsCheby2/H.C.C.H (kjmol au)
fc = +- sgn = -1
Oopdist/C.C.H.C (kjmol/A^2 A)
fc = +- rv = .0000 +- .000
EQSET Averaging force field parameters over master and slaves
PTGEN Resetting system coordinates to ab initio ref
PTGEN Constructing trajectories
PTEST Resetting system coordinates to ab initio ref
PTEST Estimating FF parameters from perturbation trajectories
PTEST rest value of Oopdist/C.C.H.C was negative: set to zero
PTEST rest value of Oopdist/C.C.H.C was negative: set to zero
PTEST rest value of Oopdist/C.C.H.C was negative: set to zero
PTEST rest value of Oopdist/C.C.H.C was negative: set to zero
PTEST rest value of Oopdist/C.C.H.C was negative: set to zero
PTEST rest value of Oopdist/C.C.H.C was negative: set to zero
BondHarm/C.C (kjmol/A^2 A)
fc = 4775 +- .038 rv = 1.397 +- .000
BondHarm/C.H (kjmol/A^2 A)
fc = 3365 +- .078 rv = 1.090 +- .000
BendAHarm/C.C.C (kjmol/rad^2 deg)
fc = 3011 +- .036 rv = 120.0 +- .000
BendAHarm/C.C.H (kjmol/rad^2 deg)
fc = 641.4 +- .023 rv = 120.0 +- .000
TorsCheby2/C.C.C.C (kjmol au)
fc = +- sgn = -1
TorsCheby2/C.C.C.H (kjmol au)
fc = +- sgn = -1
TorsCheby2/H.C.C.H (kjmol au)
fc = +- sgn = -1
Oopdist/C.C.H.C (kjmol/A^2 A)
fc = 1519 +- .384 rv = .0000 +- .000
PTPOST Averaging force field parameters over master and slaves
VAL Resetting system coordinates to ab initio ref
VAL Added 18 stretch-stretch and 36 stretch-angle cross terms from angle
VAL patterns
HCEST Resetting system coordinates to ab initio ref
HCEST Estimating force constants from Hessian cost for tasks HC_FC_DIAG HC_FC_
HCEST CROSS_ASS HC_FC_CROSS_ASA
BondHarm/C.C (kjmol/A^2 A)
fc = 4015 +- .000 rv = 1.397 +- .000
BondHarm/C.H (kjmol/A^2 A)
fc = 3367 +- .000 rv = 1.090 +- .000
BendAHarm/C.C.C (kjmol/rad^2 deg)
fc = 597.8 +- .000 rv = 120.0 +- .000
BendAHarm/C.C.H (kjmol/rad^2 deg)
fc = 327.2 +- .000 rv = 120.0 +- .000
TorsCheby2/C.C.C.C (kjmol au)
fc = 34.9 +- 0.0 sgn = -1
TorsCheby2/C.C.C.H (kjmol au)
fc = 31.8 +- 0.0 sgn = -1
TorsCheby2/H.C.C.H (kjmol au)
fc = 16.7 +- 0.0 sgn = -1
Oopdist/C.C.H.C (kjmol/A^2 A)
fc = 162.9 +- .000 rv = .0000 +- .000
Cross/C.C.C/b0a (kjmol/A A deg)
fc = 43.5 +- .0 rv0 = 1.39 +- 0.0 rv1 = 120 +- .00
Cross/C.C.C/b1a (kjmol/A A deg)
fc = 43.5 +- .0 rv0 = 1.39 +- 0.0 rv1 = 120 +- .00
Cross/C.C.C/bb (kjmol/A^2 A A)
fc = 513 +- .0 rv0 = 1.39 +- 0.0 rv1 = 1.39 +- 0.0
Cross/C.C.H/b0a (kjmol/A A deg)
fc = 113 +- .0 rv0 = 1.39 +- .00 rv1 = 120 +- .00
Cross/C.C.H/b1a (kjmol/A A deg)
fc = 139 +- .0 rv0 = 1.09 +- 0.0 rv1 = 120 +- .00
Cross/C.C.H/bb (kjmol/A^2 A A)
fc = 43.6 +- .0 rv0 = 1.39 +- .00 rv1 = 1.09 +- 0.0
PTEST Resetting system coordinates to ab initio ref
PTEST Estimating FF parameters from perturbation trajectories with valence
PTEST reference
BondHarm/C.C (kjmol/A^2 A)
fc = 4020 +- .036 rv = 1.397 +- .000
BondHarm/C.H (kjmol/A^2 A)
fc = 3365 +- .078 rv = 1.090 +- .000
BendAHarm/C.C.C (kjmol/rad^2 deg)
fc = 602.9 +- .035 rv = 119.9 +- .000
BendAHarm/C.C.H (kjmol/rad^2 deg)
fc = 327.6 +- .023 rv = 120.1 +- .000
TorsCheby2/C.C.C.C (kjmol au)
fc = 34.9 +- 0.0 sgn = -1
TorsCheby2/C.C.C.H (kjmol au)
fc = 31.8 +- 0.0 sgn = -1
TorsCheby2/H.C.C.H (kjmol au)
fc = 16.7 +- 0.0 sgn = -1
Oopdist/C.C.H.C (kjmol/A^2 A)
fc = 147.2 +- .319 rv = .0000 +- .000
Cross/C.C.C/b0a (kjmol/A A deg)
fc = 43.5 +- .0 rv0 = 1.39 +- 0.0 rv1 = 120 +- .00
Cross/C.C.C/b1a (kjmol/A A deg)
fc = 43.5 +- .0 rv0 = 1.39 +- 0.0 rv1 = 120 +- .00
Cross/C.C.C/bb (kjmol/A^2 A A)
fc = 513 +- .0 rv0 = 1.39 +- 0.0 rv1 = 1.39 +- 0.0
Cross/C.C.H/b0a (kjmol/A A deg)
fc = 113 +- .0 rv0 = 1.39 +- .00 rv1 = 120 +- .00
Cross/C.C.H/b1a (kjmol/A A deg)
fc = 139 +- .0 rv0 = 1.09 +- 0.0 rv1 = 120 +- .00
Cross/C.C.H/bb (kjmol/A^2 A A)
fc = 43.6 +- .0 rv0 = 1.39 +- .00 rv1 = 1.09 +- 0.0
PTPOST Averaging force field parameters over master and slaves
HCEST Resetting system coordinates to ab initio ref
HCEST Estimating force constants from Hessian cost for tasks HC_FC_DIAG HC_FC_
HCEST CROSS_ASS HC_FC_CROSS_ASA
BondHarm/C.C (kjmol/A^2 A)
fc = 4015 +- .000 rv = 1.397 +- .000
BondHarm/C.H (kjmol/A^2 A)
fc = 3367 +- .000 rv = 1.090 +- .000
BendAHarm/C.C.C (kjmol/rad^2 deg)
fc = 598.9 +- .000 rv = 119.9 +- .000
BendAHarm/C.C.H (kjmol/rad^2 deg)
fc = 327.5 +- .000 rv = 120.1 +- .000
TorsCheby2/C.C.C.C (kjmol au)
fc = 35.4 +- 0.0 sgn = -1
TorsCheby2/C.C.C.H (kjmol au)
fc = 31.9 +- .00 sgn = -1
TorsCheby2/H.C.C.H (kjmol au)
fc = 16.7 +- 0.0 sgn = -1
Oopdist/C.C.H.C (kjmol/A^2 A)
fc = 158.3 +- .000 rv = .0000 +- .000
Cross/C.C.C/b0a (kjmol/A A deg)
fc = 43.4 +- .0 rv0 = 1.39 +- 0.0 rv1 = 119 +- .00
Cross/C.C.C/b1a (kjmol/A A deg)
fc = 43.4 +- .0 rv0 = 1.39 +- 0.0 rv1 = 119 +- .00
Cross/C.C.C/bb (kjmol/A^2 A A)
fc = 513 +- .0 rv0 = 1.39 +- 0.0 rv1 = 1.39 +- 0.0
Cross/C.C.H/b0a (kjmol/A A deg)
fc = 113 +- .0 rv0 = 1.39 +- 0.0 rv1 = 120 +- 0.0
Cross/C.C.H/b1a (kjmol/A A deg)
fc = 139 +- .0 rv0 = 1.09 +- .00 rv1 = 120 +- 0.0
Cross/C.C.H/bb (kjmol/A^2 A A)
fc = 43.6 +- .0 rv0 = 1.39 +- 0.0 rv1 = 1.09 +- .00
HCEST Resetting system coordinates to ab initio ref
HCEST Estimating force constants from Hessian cost for tasks HC_FC_CROSS_ASS
HCEST HC_FC_CROSS_ASA HC_FC_CROSS_DSS HC_FC_CROSS_DSD HC_FC_CROSS_DAA HC_FC_
HCEST CROSS_DAD
BondHarm/C.C (kjmol/A^2 A)
fc = 4015 +- .000 rv = 1.397 +- .000
BondHarm/C.H (kjmol/A^2 A)
fc = 3367 +- .000 rv = 1.090 +- .000
BendAHarm/C.C.C (kjmol/rad^2 deg)
fc = 598.9 +- .000 rv = 119.9 +- .000
BendAHarm/C.C.H (kjmol/rad^2 deg)
fc = 327.5 +- .000 rv = 120.1 +- .000
TorsCheby2/C.C.C.C (kjmol au)
fc = 35.4 +- 0.0 sgn = -1
TorsCheby2/C.C.C.H (kjmol au)
fc = 31.9 +- .00 sgn = -1
TorsCheby2/H.C.C.H (kjmol au)
fc = 16.7 +- 0.0 sgn = -1
Oopdist/C.C.H.C (kjmol/A^2 A)
fc = 158.3 +- .000 rv = .0000 +- .000
Cross/C.C.C/b0a (kjmol/A A deg)
fc = 43.4 +- .0 rv0 = 1.39 +- 0.0 rv1 = 119 +- .00
Cross/C.C.C/b1a (kjmol/A A deg)
fc = 43.4 +- .0 rv0 = 1.39 +- 0.0 rv1 = 119 +- .00
Cross/C.C.C/bb (kjmol/A^2 A A)
fc = 513 +- .0 rv0 = 1.39 +- 0.0 rv1 = 1.39 +- 0.0
Cross/C.C.H/b0a (kjmol/A A deg)
fc = 113 +- .0 rv0 = 1.39 +- 0.0 rv1 = 120 +- 0.0
Cross/C.C.H/b1a (kjmol/A A deg)
fc = 139 +- .0 rv0 = 1.09 +- .00 rv1 = 120 +- 0.0
Cross/C.C.H/bb (kjmol/A^2 A A)
fc = 43.6 +- .0 rv0 = 1.39 +- 0.0 rv1 = 1.09 +- .00
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TIMING Initializing 0:00:00.267873
TIMING Equil Set RV 0:00:00.003699
TIMING PT Generate 0:00:08.043499
TIMING PT Estimate 0:00:00.315404
TIMING PT Post process 0:00:00.003995
TIMING HC Estimate FC 0:00:00.490931
__/\\\__________________________________________________________________/\\\____
\ \\\ \ \\\
\ \\\ End of file. Thanks for using QuickFF! Come back soon!! \ \\\
____\///__________________________________________________________________\///__