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update and rerun test cases for Tinker 25.5 release
1 parent e84169d commit f833f0b

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-14155
lines changed

‎test/0README‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -15,18 +15,18 @@
1515

1616
(1) ANION Estimates the hydration free energy difference for
1717
Cl- vs. Br- anion via a 10 picosecond simulation
18-
of a "hybrid" anion in a box of water, followed by
19-
free energy perturbation
18+
of a "hybrid" anion in a box of flexible SPC water,
19+
followed by free energy perturbation
2020

2121
(2) ARGON Performs an initial energy minimization on a periodic
2222
box containing 150 argon atoms, then performs 25
2323
picoseconds of molecular dynamics simulation, on a
2424
box with 150 argon atoms
2525

2626
(3) CATION Computes the hydration free energy difference for
27-
Rb+ vs. Cs+ cation via a 2 picosecond simulation
28-
of each cation in a box of water, followed by a BAR
29-
free energy calculation
27+
Rb+ vs. Cs+ cation via a 10 picosecond simulation of
28+
each cation in a box of AMOEBA water, followed by a
29+
BAR free energy calculation
3030

3131
(4) CLUSTER Performs 10 Gaussian density annealing (GDA)trials on
3232
a cluster of 13 argon atoms to find the global minimum

‎test/anion.log‎

Lines changed: 5241 additions & 5235 deletions
Large diffs are not rendered by default.

‎test/argon.log‎

Lines changed: 300 additions & 300 deletions
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‎test/cation.ckey‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ thermostat BUSSI
88

99
neighbor-list
1010
list-buffer 0.2
11-
vdw-cutoff 9.0
11+
vdw-cutoff 8.5
1212
ewald
1313
ewald-cutoff 7.0
1414

‎test/cation.log‎

Lines changed: 13268 additions & 2397 deletions
Large diffs are not rendered by default.

‎test/cation.rkey‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ thermostat BUSSI
88

99
neighbor-list
1010
list-buffer 0.2
11-
vdw-cutoff 9.0
11+
vdw-cutoff 8.5
1212
ewald
1313
ewald-cutoff 7.0
1414

‎test/cation.run‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,8 @@ cp cation.rxyz cationr.xyz
22
cp cation.rkey cationr.key
33
cp cation.cxyz cationc.xyz
44
cp cation.ckey cationc.key
5-
../bin/dynamic cationr 1000 2.0 0.1 2 300.0
6-
../bin/dynamic cationc 1000 2.0 0.1 2 300.0
7-
../bin/bar 1 cationr.arc 300.0 cationc.arc 300.0 N
8-
../bin/bar 2 cationr.bar 1 20 1 1 20 1
5+
../bin/dynamic cationr 5000 2.0 0.1 2 298.0
6+
../bin/dynamic cationc 5000 2.0 0.1 2 298.0
7+
../bin/bar 1 cationr.arc 298.0 cationc.arc 298.0 N
8+
../bin/bar 2 cationr.bar 1 100 1 1 100 1
99
rm cationr.* cationc.*

‎test/clean.make‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -26,4 +26,4 @@ rm methanol.xyz* methanol.key_*
2626
rm polyala.xyz* polyala.int* polyala.seq* polyala.arc*
2727
rm pyridine.xyz_*
2828
rm salt.xyz*
29-
rm water.key
29+
rm water.key*

‎test/cluster.log‎

Lines changed: 32 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -68,7 +68,7 @@
6868
26 2.0585 -1.3882 5.3236 -0.1170 Retry
6969
27 2.0817 -2.4378 5.0266 -0.2321 Success
7070
28 2.1157 -4.3147 4.6209 -0.4393 Success
71-
29 2.1376 -5.5685 4.4032 -0.5933 Success
71+
29 2.1376 -5.5684 4.4032 -0.5933 Success
7272
30 2.1738 -7.2633 4.1485 -0.8556 Success
7373
31 2.2077 -8.2738 4.0091 -1.0814 Success
7474
32 2.2555 -9.0346 3.9050 -1.3450 Success
@@ -135,7 +135,7 @@
135135
83 -11.6665 0.2395 0.2722 0.3271 2 NegCurve 10
136136
84 -11.8287 0.2092 0.1622 0.3051 4 NegCurve 15
137137
85 -12.1761 0.3610 0.3475 0.5637 5 NegCurve 21
138-
86 -12.4056 0.2501 0.2294 0.3082 15 TruncNewt 34
138+
86 -12.4056 0.2501 0.2294 0.3083 15 TruncNewt 34
139139
87 -12.5157 0.0343 0.1101 0.1265 21 TruncNewt 42
140140
88 -12.5179 0.0014 0.0022 0.0186 25 TruncNewt 47
141141
89 -12.5179 0.0000 0.0000 0.0005 31 TruncNewt 54
@@ -210,7 +210,7 @@
210210
59 7.2296 -10.9717 3.6924 -7.1960 Success
211211
60 7.4475 -10.9915 3.6908 -7.4141 Success
212212
61 7.6655 -11.0110 3.6893 -7.6323 Success
213-
62 7.8835 -11.0303 3.6879 -7.8504 Success
213+
62 7.8834 -11.0303 3.6879 -7.8504 Success
214214
63 8.1013 -11.0492 3.6865 -8.0684 Success
215215
64 8.3192 -11.0677 3.6851 -8.2865 Success
216216
65 8.5370 -11.0856 3.6838 -8.5045 Success
@@ -474,7 +474,7 @@
474474
10 0.7708 20.2676 19.0377 1.9349 Success
475475
11 0.8429 18.4599 18.6602 1.8290 Success
476476
12 0.9115 16.5236 18.0907 1.7021 Success
477-
13 0.9537 15.1337 17.7083 1.6060 Retry
477+
13 0.9537 15.1336 17.7083 1.6060 Retry
478478
14 0.9885 13.7088 17.3336 1.5031 Success
479479
15 1.0242 12.4602 16.8051 1.4105 Retry
480480
16 1.0616 11.4428 16.2024 1.3367 Success
@@ -489,10 +489,10 @@
489489
25 1.8529 2.2914 7.6667 0.3799 Success
490490
26 1.9173 1.7034 7.0963 0.2820 Success
491491
27 1.9569 1.2332 6.7180 0.2087 Success
492-
28 1.9905 0.7051 6.3709 0.1329 Retry
492+
28 1.9905 0.7050 6.3709 0.1329 Retry
493493
29 2.0187 0.1094 6.0569 0.0552 Success
494494
30 2.0449 -0.6265 5.7475 -0.0321 Retry
495-
31 2.0669 -1.4139 5.4787 -0.1188 Success
495+
31 2.0669 -1.4140 5.4787 -0.1188 Success
496496
32 2.0987 -2.8331 5.0910 -0.2706 Success
497497
33 2.1195 -3.8721 4.8557 -0.3891 Success
498498
34 2.1531 -5.4749 4.5414 -0.6048 Success
@@ -564,11 +564,11 @@
564564
90 -11.3016 0.2392 0.1666 0.2627 4 NegCurve 21
565565
91 -11.7229 0.3768 0.4212 0.5752 5 NegCurve 27
566566
92 -12.1980 0.3262 0.4751 0.2249 6 NegCurve 31
567-
93 -12.3879 0.2689 0.1899 0.1896 14 NegCurve 42
568-
94 -12.3992 0.2521 0.0113 0.2471 20 NegCurve 56
569-
95 -12.5121 0.0677 0.1129 0.1106 26 TruncNewt 66
570-
96 -12.5179 0.0036 0.0058 0.0204 29 TruncNewt 70
571-
97 -12.5179 0.0000 0.0000 0.0013 34 TruncNewt 76
567+
93 -12.3846 0.2701 0.1866 0.2014 14 NegCurve 42
568+
94 -12.4447 0.1952 0.0600 0.3634 20 NegCurve 53
569+
95 -12.5162 0.0328 0.0716 0.0638 24 TruncNewt 60
570+
96 -12.5179 0.0011 0.0017 0.0121 27 TruncNewt 64
571+
97 -12.5179 0.0000 0.0000 0.0005 32 TruncNewt 70
572572

573573
TNCG -- Normal Termination due to SmallGrad
574574

@@ -785,9 +785,9 @@
785785
85 -11.6742 0.3775 0.2056 0.3972 18 NegCurve 34
786786
86 -12.2876 0.3020 0.6135 0.4462 19 NegCurve 39
787787
87 -12.4733 0.1693 0.1857 0.1689 23 NegCurve 46
788-
88 -12.4891 0.1325 0.0158 0.2647 29 NegCurve 56
788+
88 -12.4891 0.1324 0.0158 0.2648 29 NegCurve 56
789789
89 -12.5175 0.0183 0.0284 0.0533 34 NegCurve 64
790-
90 -12.5179 0.0004 0.0004 0.0046 37 TruncNewt 68
790+
90 -12.5179 0.0004 0.0004 0.0045 37 TruncNewt 68
791791
91 -12.5179 0.0000 0.0000 0.0001 43 TruncNewt 75
792792

793793
TNCG -- Normal Termination due to SmallGrad
@@ -815,7 +815,7 @@
815815
13 0.9309 12.2343 16.7622 1.4397 Success
816816
14 1.0299 10.2608 15.3622 1.3133 Success
817817
15 1.1452 8.3851 13.8809 1.1761 Success
818-
16 1.2515 6.9700 12.6475 1.0549 Success
818+
16 1.2515 6.9701 12.6475 1.0549 Success
819819
17 1.3773 5.6006 11.3325 0.9153 Success
820820
18 1.4835 4.6460 10.3276 0.7990 Success
821821
19 1.6034 3.7305 9.2869 0.6679 Success
@@ -892,14 +892,14 @@
892892
TN Iter F Value G RMS F Move X Move CG Iter Solve FG Call
893893

894894
82 -11.4230 0.0361 1
895-
83 -11.4268 0.0332 0.0038 0.1117 6 NegCurve 11
896-
84 -11.4876 0.1771 0.0608 0.3413 11 NegCurve 20
897-
85 -11.6935 0.3055 0.2059 0.3253 12 NegCurve 25
898-
86 -11.9153 0.2719 0.2218 0.2419 14 NegCurve 31
899-
87 -12.1728 0.3021 0.2574 0.2985 15 NegCurve 35
900-
88 -12.4302 0.1880 0.2574 0.3141 19 NegCurve 42
901-
89 -12.5083 0.0688 0.0781 0.1126 25 NegCurve 50
902-
90 -12.5178 0.0063 0.0095 0.0286 28 TruncNewt 54
895+
83 -11.4268 0.0332 0.0038 0.1116 6 NegCurve 11
896+
84 -11.4876 0.1771 0.0608 0.3414 11 NegCurve 20
897+
85 -11.6942 0.3057 0.2065 0.3259 12 NegCurve 25
898+
86 -11.9136 0.2724 0.2195 0.2406 14 NegCurve 31
899+
87 -12.1708 0.3020 0.2572 0.2983 15 NegCurve 35
900+
88 -12.4293 0.1885 0.2584 0.3152 19 NegCurve 42
901+
89 -12.5081 0.0695 0.0789 0.1107 25 NegCurve 50
902+
90 -12.5178 0.0064 0.0097 0.0288 28 TruncNewt 54
903903
91 -12.5179 0.0001 0.0001 0.0027 32 TruncNewt 59
904904

905905
TNCG -- Normal Termination due to SmallGrad
@@ -1108,16 +1108,16 @@
11081108

11091109
81 -11.2476 0.1031 1
11101110
82 -11.3583 0.1297 0.1107 0.2917 2 ScaleStep 8
1111-
83 -11.4261 0.0501 0.0678 0.2195 18 NegCurve 26
1112-
84 -11.4397 0.0433 0.0136 0.1965 30 NegCurve 40
1113-
85 -11.4461 0.0396 0.0064 0.1808 47 TruncNewt 61
1114-
86 -11.4527 0.0141 0.0066 0.1112 56 TruncNewt 73
1115-
87 -11.4582 0.0418 0.0054 0.2258 64 NegCurve 84
1116-
88 -11.5704 0.1843 0.1122 0.3414 65 NegCurve 90
1117-
89 -11.6832 0.1165 0.1128 0.2844 79 TruncNewt 107
1118-
90 -11.7115 0.0107 0.0283 0.0666 84 TruncNewt 114
1119-
91 -11.7117 0.0001 0.0002 0.0055 89 TruncNewt 120
1120-
92 -11.7117 0.0000 0.0000 0.0001 96 TruncNewt 128
1111+
83 -11.4259 0.0501 0.0677 0.2183 16 TruncNewt 24
1112+
84 -11.4383 0.0426 0.0123 0.2089 28 NegCurve 38
1113+
85 -11.4463 0.0362 0.0080 0.1649 39 TruncNewt 52
1114+
86 -11.4527 0.0150 0.0064 0.1161 48 TruncNewt 64
1115+
87 -11.4531 0.0108 0.0003 0.1017 56 NegCurve 74
1116+
88 -11.5360 0.1920 0.0830 0.4596 66 NegCurve 91
1117+
89 -11.6546 0.1817 0.1185 0.3457 77 TruncNewt 103
1118+
90 -11.7107 0.0271 0.0561 0.0583 83 TruncNewt 111
1119+
91 -11.7117 0.0007 0.0010 0.0106 89 TruncNewt 118
1120+
92 -11.7117 0.0000 0.0000 0.0003 95 TruncNewt 125
11211121

11221122
TNCG -- Normal Termination due to SmallGrad
11231123

‎test/crambin.log‎

Lines changed: 23 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -287,23 +287,25 @@
287287

288288
Alternative Surface Area & Volume Methods
289289

290-
Number of Atoms : 642
291-
Probe Size : 1.4000
290+
Number of Atoms : 642
291+
Probe Size : 1.4000
292292

293293
Timothy Richmond Accessible Surface Area Method :
294294

295-
CPU and Wall Times : 0.0709 0.0710
295+
CPU and Wall Times : 0.0761 0.0760
296296

297-
Total Surface Area : 3180.3168
297+
Total Surface Area : 3180.3168
298298

299299
Timothy Richmond Surface Area Derivative Method :
300300

301-
CPU and Wall Times : 0.0726 0.0730
301+
CPU and Wall Times : 0.0782 0.0790
302302

303-
Total Surface Area : 3180.3168
303+
Total Surface Area : 3180.3168
304304

305305
Surface Area Derivatives : (First Ten Atoms)
306306

307+
Atom dAx dAy dAz
308+
307309
1 -0.0280 -0.5361 0.4212
308310
2 0.0000 0.0000 0.0000
309311
3 0.0000 0.0000 0.0000
@@ -317,18 +319,20 @@
317319

318320
Michael Connolly Molecular Area-Volume Method :
319321

320-
CPU and Wall Times : 0.1046 0.1060
322+
CPU and Wall Times : 0.1199 0.1200
321323

322-
Total Surface Area : 3180.3169
324+
Total Surface Area : 3180.3168
323325

324-
Total Excluded Vol : 10275.3184
326+
Total Excluded Volume : 10275.3183
325327

326328
Craig Kundrot Excluded Volume Derivative Method :
327329

328-
CPU and Wall Times : 0.7929 0.7960
330+
CPU and Wall Times : 0.9376 0.9700
329331

330332
Excluded Volume Derivatives : (First Ten Atoms)
331333

334+
Atom dVx dVy dVz
335+
332336
1 0.0058 0.0912 -0.0774
333337
2 0.0000 0.0000 0.0000
334338
3 0.0000 0.0000 0.0000
@@ -342,20 +346,22 @@
342346

343347
Patrice Koehl UnionBall Alpha Shape Method :
344348

345-
CPU and Wall Times : 0.0056 0.0060
349+
CPU and Wall Times : 0.0061 0.0070
346350

347-
Total Surface Area : 3180.3168
351+
Total Surface Area : 3180.3168
348352

349-
Total Excluded Vol : 10275.3183
353+
Total Excluded Volume : 10275.3183
350354

351355
Surface Area & Volume Derivatives : (First Ten Atoms)
352356

357+
Atom dAx dAy dAz dVx dVy dVz
358+
353359
1 -0.0280 -0.5361 0.4212 0.0058 0.0912 -0.0774
354-
2 0.0000 0.0000 -0.0000 0.0000 -0.0000 -0.0000
360+
2 0.0000 0.0000 -0.0000 -0.0000 0.0000 0.0000
355361
3 -0.0000 -0.0000 0.0000 -0.0000 -0.0000 0.0000
356-
4 0.0000 -0.0000 0.0000 0.0000 -0.0000 0.0000
362+
4 0.0000 -0.0000 -0.0000 0.0000 0.0000 -0.0000
357363
5 0.2696 -1.2397 -3.6199 5.1755 1.4148 -12.7974
358-
6 -0.0000 0.0000 -0.0000 -0.0000 0.0000 -0.0000
364+
6 0.0000 0.0000 -0.0000 0.0000 0.0000 -0.0000
359365
7 1.1530 0.3285 1.2856 0.0053 2.0817 -8.3273
360366
8 2.0763 -1.4381 -0.7206 2.2062 -7.6297 -10.6676
361367
9 0.0000 -0.0000 -0.0000 0.0000 -0.0000 -0.0000
@@ -511,7 +517,7 @@
511517

512518
Convex Faces : 344 Area : 939.791 Volume : 524.811
513519
Saddle Faces : 1026 Area : 1031.640 Volume : 962.447
514-
Concave Faces : 684 Area : 528.204 Volume : 1054.488
520+
Concave Faces : 684 Area : 528.205 Volume : 1054.488
515521
Buried Polyhedra : Volume : 3763.353
516522

517523
Spindle Correction : Area : 3.579 Volume : -0.661

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