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Commit 70d872fe authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
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sPuReMD: clean-up EE and ACKS2 codes.

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......@@ -19,6 +19,7 @@
# ViM, emacs, nano, leafpad
*.swp
*~
tags
# Python
*.pyc
......@@ -54,7 +55,12 @@ stamp-h1
*.tab.c
*.tab.h
# PBS/torque job logs
*.o[0-9]*
*.e[0-9]*
# General
*.tar.gz
*.pdf
*/bin
*.txt
data/benchmarks/water/ffield_Achtyl 0 → 100644
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Reactive MD-force field: water/C/Ca/Ti AKS2 July 18; water from Feb 29
39 ! Number of general parameters
50.0000 !Overcoordination parameter
9.5469 !Overcoordination parameter
1.6725 !Valency angle conjugation parameter
1.7224 !Triple bond stabilisation parameter
6.8702 !Triple bond stabilisation parameter
54.6742 !C2-correction
1.0588 !Undercoordination parameter
4.6000 !Triple bond stabilisation parameter
12.1176 !Undercoordination parameter
13.3056 !Undercoordination parameter
-34.5448 !Triple bond stabilization energy
0.0000 !Lower Taper-radius
10.0000 !Upper Taper-radius
2.8793 !Not used
33.8667 !Valency undercoordination
6.0891 !Valency angle/lone pair parameter
1.0563 !Valency angle
2.0384 !Valency angle parameter
6.1431 !Not used
6.9290 !Double bond/angle parameter
0.3989 !Double bond/angle parameter: overcoord
3.9954 !Double bond/angle parameter: overcoord
-2.4837 !Not used
8.5385 !Torsion/BO parameter
6.7491 !Torsion overcoordination
0.1414 !Torsion overcoordination
-1.2327 !Conjugation 0 (not used)
1.1348 !Conjugation
1.5591 !vdWaals shielding
0.1000 !Cutoff for bond order (*100)
1.7602 !Valency angle conjugation parameter
0.6991 !Overcoordination parameter
50.0000 !Overcoordination parameter
1.8512 !Valency/lone pair parameter
548.6451 !Softness
0.0000 !Cutoff
5.0000 !Molecular energy (not used)
0.0000 !Molecular energy (not used)
0.7903 !Valency angle conjugation parameter
13 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;#
alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u.
cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u.
ov/un;val1;n.u.;val3,vval4
C 1.3417 4.0000 12.0000 2.0464 0.1064 0.4670 1.1681 4.0000
9.0000 1.5000 4.0000 40.0000 79.5548 5.3422 4.5000 0.0000
1.1437 0.0000 181.0000 5.4236 19.2788 13.5366 3.1838 0.0000
-4.0998 4.8750 1.0564 4.0000 2.9663 1.2500 0.4000 21.3612
H 0.9102 1.0000 1.0080 1.0996 0.1000 0.6683 -0.1000 1.0000
9.2193 5.5154 1.0000 0.0000 121.1250 4.9673 6.2079 0.0000
-0.1000 0.0000 55.5000 1.1004 6.8959 0.0003 3.4114 0.0000
-6.5532 3.5000 1.0338 1.0000 2.8793 0.5000 0.1000 1.0000
O 1.2218 2.0000 15.9990 2.2033 0.2841 0.9750 1.0727 6.0000
8.8250 200.0000 4.0000 37.5000 116.0768 8.5000 7.9071 0.0000
0.9049 0.5488 68.0152 2.1943 2.3055 0.0021 5.4479 0.0000
-6.0011 3.6068 1.0493 4.0000 2.9225 0.5000 0.1000 1.0000
N 1.2333 3.0000 14.0000 2.2375 0.1447 1.0000 1.1748 5.0000
9.8626 12.6599 4.0000 30.3181 100.0000 6.0111 6.7037 0.0000
1.0433 0.7872 119.9837 0.7425 6.7920 2.7271 2.2882 0.0000
-2.0000 4.0000 1.0183 4.0000 2.8793 1.0000 0.1000 1.0000
S 1.9405 2.0000 32.0600 2.0677 0.2099 1.0336 1.5479 6.0000
9.9575 4.9055 4.0000 52.9998 112.1416 6.5000 8.2545 0.0000
1.4601 9.7177 71.1843 5.7487 23.2859 12.7147 2.2882 0.0000
-11.0000 2.7466 1.0338 6.2998 2.8793 1.0000 0.1000 10.0000
Mg 1.8315 2.0000 24.3050 2.2464 0.1806 0.5020 1.0000 2.0000
10.9186 27.1205 3.0000 38.0000 0.0000 0.9499 5.6130 0.0000
-1.3000 0.0000 127.9160 49.9248 0.3370 0.0000 2.2882 0.0000
-1.0823 2.3663 1.0564 6.0000 2.9663 1.0000 0.1000 10.0000
P 1.5994 3.0000 30.9738 1.7000 0.1743 1.0000 1.3000 5.0000
9.1909 14.9482 5.0000 0.0000 0.0000 1.6676 7.0946 0.0000
-1.0000 25.0000 125.6300 0.2187 21.4305 15.1425 2.2882 0.0000
-3.9294 3.4831 1.0338 5.0000 2.8793 1.0000 0.1000 10.0000
Na 1.8000 1.0000 22.9898 2.8270 0.1872 0.4000 -1.0000 1.0000
10.0000 2.5000 1.0000 0.0000 0.0000 -0.9871 6.7728 0.0000
-1.0000 0.0000 23.0445 100.0000 1.0000 0.0000 2.2882 0.0000
-2.5000 3.9900 1.0338 8.0000 2.5791 1.0000 0.1000 10.0000
Ti 2.0254 4.0000 47.8800 2.2105 0.1574 0.6311 0.1000 4.0000
12.7041 16.6482 4.0000 0.1000 0.0000 -1.3647 6.8406 0.0000
-1.0000 0.0000 143.1770 27.6505 -0.0753 0.0064 2.2882 0.0000
-15.0000 3.8359 1.0338 12.0000 2.2632 1.0000 0.1000 10.0000
Cl 1.7140 1.0000 35.4500 1.9139 0.2000 0.3500 -1.0000 7.0000
11.5345 10.1330 1.0000 0.0000 0.0000 9.9704 6.1703 0.0000
-1.0000 1.2769 143.1770 6.2293 5.2294 0.1542 2.2882 0.0000
-10.2080 2.9867 1.0338 6.2998 2.5791 1.0000 0.1000 10.0000
F 1.2100 1.0000 18.9984 1.8601 0.1200 0.3000 -0.1000 7.0000
11.5000 7.5000 4.0000 9.2533 0.2000 9.0000 15.0000 0.0000
-1.0000 35.0000 1.5000 6.9821 4.1799 1.0561 2.2882 0.0000
-7.3000 2.6656 1.0493 4.0000 2.9225 1.0000 0.1000 10.0000
Ca 1.9058 2.0000 40.0870 2.3698 0.3719 0.6038 -1.0000 2.0000
9.8681 5.0000 3.0000 38.0000 0.0000 -5.7471 7.3556 0.0000
-1.3000 0.0000 220.0000 49.9248 0.3370 0.0000 3.7000 0.0000
-3.9745 3.0069 1.0564 8.0000 2.9663 0.5000 0.1000 10.0000
X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000
10.0000 2.5000 4.0000 0.0000 0.0000 -0.1000 25.0000 0.0000
-0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.1000 0.0000
-11.0000 2.7466 1.0338 4.0000 2.8793 1.0000 0.1000 10.0000
62 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6
pbe2;pbo3;pbo4;Etrip;pbo1;pbo2;ovcorr
1 1 78.4266 115.3834 68.1631 0.5777 -0.2901 1.0000 34.9989 0.5101
3.8560 -0.1640 8.2326 1.0000 -0.0585 6.7997 1.0000 0.0000
1 2 191.4398 0.0000 0.0000 -0.6539 0.0000 1.0000 6.0000 0.4898
6.3962 1.0000 0.0000 1.0000 -0.0607 6.9960 0.0000 0.0000
2 2 161.2898 0.0000 0.0000 -0.2387 0.0000 1.0000 6.0000 0.6279
13.2089 1.0000 0.0000 1.0000 -0.1674 6.9118 0.0000 0.0000
1 3 170.8787 152.2997 125.6008 0.2914 -0.2305 1.0000 16.7601 0.8645
3.9615 -0.5703 7.4065 1.0000 -0.2514 4.5085 0.0000 0.0000
3 3 222.6268 93.7249 50.8293 0.5588 -0.1000 1.0000 29.7503 0.0125
0.5865 -0.2030 9.1777 1.0000 -0.1357 6.4747 1.0000 0.0000
1 4 163.8300 145.4458 89.6879 -1.3368 -0.3468 1.0000 27.5160 0.1575
0.1817 -0.3114 7.1789 1.0000 -0.2345 4.5111 1.0000 0.0000
3 4 130.8596 169.4551 40.0000 0.3837 -0.1639 1.0000 35.0000 0.2000
1.0000 -0.3579 7.0004 1.0000 -0.1193 6.8773 1.0000 0.0000
4 4 157.9384 82.5526 152.5336 0.4010 -0.1034 1.0000 12.4261 0.5828
0.1578 -0.1509 11.9186 1.0000 -0.0861 5.4271 1.0000 0.0000
2 3 143.3409 0.0000 0.0000 -0.4886 0.0000 1.0000 6.0000 0.3927
1.3588 1.0000 0.0000 0.0000 -0.0781 4.0330 0.0000 0.0000
2 4 210.1187 0.0000 0.0000 -0.3705 0.0000 1.0000 6.0000 0.3284
5.8196 1.0000 0.0000 1.0000 -0.1104 5.5184 0.0000 0.0000
1 5 128.9942 74.5848 55.2528 0.1035 -0.5211 1.0000 18.9617 0.6000
0.2949 -0.2398 8.1175 1.0000 -0.1029 5.6731 1.0000 0.0000
2 5 151.5159 0.0000 0.0000 -0.4721 0.0000 1.0000 6.0000 0.6000
9.4366 1.0000 0.0000 1.0000 -0.0290 7.0050 1.0000 0.0000
3 5 0.0000 0.0000 0.0000 0.5563 -0.4038 1.0000 49.5611 0.6000
0.4259 -0.4577 12.7569 1.0000 -0.1100 7.1145 1.0000 0.0000
4 5 0.0000 0.0000 0.0000 0.4438 -0.2034 1.0000 40.3399 0.6000
0.3296 -0.3153 9.1227 1.0000 -0.1805 5.6864 1.0000 0.0000
5 5 96.1871 93.7006 68.6860 0.0955 -0.4781 1.0000 17.8574 0.6000
0.2723 -0.2373 9.7875 1.0000 -0.0950 6.4757 1.0000 0.0000
2 6 58.6896 0.0000 0.0000 -0.0203 -0.1418 1.0000 13.1260 0.0230
8.2136 -0.1310 0.0000 1.0000 -0.2692 6.4254 0.0000 24.4461
3 6 87.0227 0.0000 43.3991 0.0030 -0.3000 1.0000 36.0000 0.0250
0.0087 -0.2500 12.0000 1.0000 -0.0439 6.6073 1.0000 24.4461
6 6 32.3808 0.0000 0.0000 -0.0076 -0.2000 0.0000 16.0000 0.2641
4.8726 -0.2000 10.0000 1.0000 -0.0729 4.6319 0.0000 0.0000
1 7 110.0000 92.0000 0.0000 0.2171 -0.1418 1.0000 13.1260 0.6000
0.3601 -0.1310 10.7257 1.0000 -0.0869 5.3302 1.0000 0.0000
2 7 0.1466 0.0000 0.0000 0.2250 -0.1418 1.0000 13.1260 0.6000
0.3912 -0.1310 0.0000 1.0000 -0.1029 9.3302 0.0000 0.0000
3 7 201.0058 194.1410 0.0000 1.0000 -0.5000 1.0000 25.0000 0.4873
0.4358 -0.1571 15.8745 1.0000 -0.2431 6.3823 1.0000 0.0000
4 7 130.0000 0.0000 0.0000 0.2171 -0.1418 1.0000 13.1260 0.6000
0.3601 -0.1310 10.7257 1.0000 -0.0869 5.3302 1.0000 0.0000
6 7 0.1000 0.0000 0.0000 0.2500 -0.5000 1.0000 35.0000 0.6000
0.5000 -0.5000 20.0000 1.0000 -0.2000 10.0000 1.0000 0.0000
7 7 0.0000 0.0000 0.0000 0.2171 -0.5000 1.0000 35.0000 0.6000
0.5000 -0.5000 20.0000 1.0000 -0.2000 10.0000 1.0000 0.0000
1 8 0.0000 0.0000 0.0000 -1.0000 -0.3000 1.0000 36.0000 0.7000
10.1151 -0.3500 25.0000 1.0000 -0.1053 8.2003 1.0000 0.0000
2 8 0.0000 0.0000 0.0000 -1.0000 -0.3000 1.0000 36.0000 0.7000
10.1151 -0.3500 25.0000 1.0000 -0.1053 8.2003 1.0000 0.0000
3 8 45.8933 0.0000 0.0000 -0.1511 -0.3000 1.0000 36.0000 0.3105
5.8448 -0.3500 25.0000 1.0000 -0.0659 7.9140 1.0000 0.0000
4 8 0.0000 0.0000 0.0000 -1.0000 -0.3000 1.0000 36.0000 0.7000
10.1151 -0.3500 25.0000 1.0000 -0.1053 8.2003 1.0000 0.0000
5 8 0.0000 0.0000 0.0000 -1.0000 -0.3000 1.0000 36.0000 0.7000
10.1151 -0.3500 25.0000 1.0000 -0.1053 8.2003 1.0000 0.0000
6 8 0.0000 0.0000 0.0000 0.2500 -0.5000 1.0000 35.0000 0.6000
0.5000 -0.5000 20.0000 1.0000 -0.2000 10.0000 1.0000 0.0000
7 8 0.0000 0.0000 0.0000 0.2500 -0.5000 1.0000 35.0000 0.6000
0.5000 -0.5000 20.0000 1.0000 -0.2000 10.0000 1.0000 0.0000
8 8 64.4508 0.0000 0.0000 -0.3738 0.3000 0.0000 25.0000 0.2158
0.9915 -0.4000 12.0000 1.0000 -0.0515 5.0000 0.0000 0.0000
4 6 50.0000 10.0901 0.0000 -1.0000 -0.3000 1.0000 36.0000 0.7058
0.8567 -0.3487 17.4990 1.0000 -0.0794 8.2232 1.0000 0.0000
1 9 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
2 9 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
3 9 130.5629 37.6984 0.0000 0.9228 -0.3000 0.0000 36.0000 0.0850
0.1150 -0.2818 16.1571 1.0000 -0.1343 6.8264 0.0000 0.0000
4 9 130.5629 37.6984 0.0000 0.9228 -0.3000 0.0000 36.0000 0.0850
0.1150 -0.2818 16.1571 1.0000 -0.1343 6.8264 0.0000 0.0000
5 9 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
6 9 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
7 9 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
8 9 0.1000 0.0000 0.0000 0.2500 -0.5000 1.0000 35.0000 0.6000
0.5000 -0.5000 20.0000 1.0000 -0.2000 10.0000 1.0000 0.0000
9 9 80.1930 0.0000 0.0000 -0.8469 -0.2000 0.0000 16.0000 0.2022
0.7528 -0.1924 14.9725 1.0000 -0.0885 5.0000 0.0000 0.0000
1 10 0.0000 0.0000 0.0000 0.5000 -0.2000 0.0000 16.0000 0.5000
1.0001 -0.2000 15.0000 1.0000 -0.1000 10.0000 0.0000 0.0000
2 10 98.9788 0.0000 0.0000 -0.0572 -0.2000 0.0000 16.0000 1.1523
2.2822 -0.2000 15.0000 1.0000 -0.1093 5.1686 0.0000 0.0000
3 10 0.0000 0.0000 0.0000 0.5000 -0.2000 0.0000 16.0000 0.5000
1.0001 -0.2000 15.0000 1.0000 -0.1000 10.0000 0.0000 0.0000
4 10 0.0000 0.0000 0.0000 0.5000 -0.2000 0.0000 16.0000 0.5000
1.0001 -0.2000 15.0000 1.0000 -0.1000 10.0000 0.0000 0.0000
5 10 0.0000 0.0000 0.0000 0.5000 -0.2000 0.0000 16.0000 0.5000
1.0001 -0.2000 15.0000 1.0000 -0.1000 10.0000 0.0000 0.0000
6 10 0.0000 0.0000 0.0000 0.5000 -0.2000 0.0000 16.0000 0.5000
1.0001 -0.2000 15.0000 1.0000 -0.1000 10.0000 0.0000 0.0000
7 10 0.0000 0.0000 0.0000 0.5000 -0.2000 0.0000 16.0000 0.5000
1.0001 -0.2000 15.0000 1.0000 -0.1000 10.0000 0.0000 0.0000
8 10 0.0000 0.0000 0.0000 0.5000 -0.2000 0.0000 16.0000 0.5000
1.0001 -0.2000 15.0000 1.0000 -0.1000 10.0000 0.0000 0.0000
9 10 0.0000 0.0000 0.0000 0.5000 -0.2000 0.0000 16.0000 0.5000
1.0001 -0.2000 15.0000 1.0000 -0.1000 10.0000 0.0000 0.0000
10 10 0.2500 0.0000 0.0000 0.1803 -0.2000 0.0000 16.0000 0.3356
0.9228 -0.2000 15.0000 1.0000 -0.1178 5.6715 0.0000 0.0000
1 11 237.8781 0.0000 0.0000 -0.7438 -0.5000 1.0000 35.0000 1.0460
3.6661 -0.2500 15.0000 1.0000 -0.0800 5.4719 1.0000 0.0000
2 11 0.0000 0.0000 0.0000 -0.4643 0.0000 1.0000 6.0000 0.6151
12.3710 1.0000 0.0000 1.0000 -0.1008 8.5980 0.0000 0.0000
3 11 0.0000 0.0000 0.0000 -0.4643 0.0000 1.0000 6.0000 0.6151
12.3710 1.0000 0.0000 1.0000 -0.1008 8.5980 0.0000 0.0000
4 11 0.0000 0.0000 0.0000 -0.4643 0.0000 1.0000 6.0000 0.6151
12.3710 1.0000 0.0000 1.0000 -0.1008 8.5980 0.0000 0.0000
5 11 0.0000 0.0000 0.0000 -0.4643 0.0000 1.0000 6.0000 0.6151
12.3710 1.0000 0.0000 1.0000 -0.1008 8.5980 0.0000 0.0000
11 11 250.0765 0.0000 0.0000 0.2298 -0.3500 1.0000 25.0000 0.8427
0.1167 -0.2500 15.0000 1.0000 -0.1506 7.3516 1.0000 0.0000
1 12 0.0000 0.0000 0.0000 -0.0203 -0.1418 1.0000 13.1260 0.0230
8.2136 -0.2500 20.0000 1.0000 -0.2692 6.4254 0.0000 24.4461
2 12 0.0000 0.0000 0.0000 -0.0203 -0.1418 1.0000 13.1260 0.0230
8.2136 -0.2500 20.0000 1.0000 -0.2692 6.4254 0.0000 24.4461
3 12 49.4055 0.0000 0.0000 0.9603 -0.3000 0.0000 36.0000 0.0025
0.4232 -0.2500 12.0000 1.0000 -0.1619 9.6512 0.0000 24.4461
12 12 22.8272 0.0000 0.0000 0.6166 -0.2000 0.0000 16.0000 0.8225
1.0000 -0.2000 10.0000 1.0000 -0.0831 4.2291 0.0000 0.0000
26 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2
1 2 0.1240 1.6326 9.8721 1.1578 -1.0000 -1.0000
2 3 0.0295 1.3181 10.1225 0.9069 -1.0000 -1.0000
2 4 0.1294 1.3025 9.8751 1.0415 -1.0000 -1.0000
1 3 0.2287 2.0452 9.0166 1.4046 1.1866 1.0375
1 4 0.2000 1.8828 9.7673 1.3387 1.2578 1.1539
3 4 0.1001 2.3274 9.0974 1.5236 1.0493 1.2531
1 5 0.1408 1.8161 9.9393 1.7986 1.3021 1.4031
2 5 0.0895 1.6239 10.0104 1.4640 -1.0000 -1.0000
3 5 0.1022 1.9887 10.0605 1.5799 1.4000 -1.0000
4 5 0.1505 1.9000 10.5104 1.8000 1.4000 -1.0000
2 6 0.0100 1.6000 13.2979 1.8670 -1.0000 -1.0000
3 6 0.0809 1.7000 11.4606 1.5177 -1.0000 -1.0000
3 7 0.0534 1.7520 10.4281 1.8000 1.4498 -1.0000
6 7 0.1801 1.8566 9.8498 0.1000 -1.0000 -1.0000
3 8 0.0825 1.5904 11.3396 1.5905 -1.0000 -1.0000
2 9 0.1750 1.7939 13.5000 0.0100 -1.0000 -1.0000
3 9 0.1200 1.8000 10.5000 1.6526 1.4718 -1.0000
1 9 0.2950 2.2000 11.0937 0.0100 -1.0000 -1.0000
2 10 0.0376 1.6671 9.6285 1.2123 -1.0000 -1.0000
3 10 0.1945 2.2766 11.2353 -1.0000 -1.0000 -1.0000
1 11 0.1071 1.6243 11.0402 1.3176 -1.0000 -1.0000
2 11 0.0431 1.7204 10.3632 0.5386 -1.0000 -1.0000
4 9 0.1200 1.8000 10.5000 1.6526 1.4718 -1.0000
1 12 0.2000 1.5000 14.0000 0.0010 0.0010 -1.0000
2 12 0.0100 1.0610 9.7343 0.0010 0.0010 -1.0000
3 12 0.1515 1.8913 12.5160 2.0022 -1.0000 -1.0000
98 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2
1 1 1 74.4118 38.0306 0.9605 0.0000 0.0100 36.6918 2.3203
1 1 2 67.2765 20.1739 3.3306 0.0000 0.0100 0.0000 1.1630
2 1 2 74.7224 38.7524 2.1423 0.0000 0.8474 0.0000 1.3144
1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400
1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400
2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400
1 1 3 61.1001 38.5283 0.4917 0.0000 4.2373 0.0000 2.1649
3 1 3 72.0708 27.2877 2.3068 -10.4517 0.1000 0.0000 1.6107
1 1 4 64.7353 38.2645 1.1478 0.0000 1.1834 0.0000 2.8465
3 1 4 81.0672 41.9015 0.4878 0.0000 1.1019 0.0000 1.0000
4 1 4 89.7621 43.0000 0.5895 0.0000 1.1155 0.0000 1.0000
2 1 3 61.3200 29.1602 0.9036 0.0000 1.8063 0.0000 1.4867
2 1 4 68.7361 36.7162 1.6697 0.0000 0.2000 0.0000 3.0000
1 2 4 0.0000 0.0019 6.3000 0.0000 0.0000 0.0000 1.0400
1 3 1 74.2533 41.5372 0.4237 0.0000 2.3660 0.0000 1.0319
1 3 3 82.8809 21.0869 3.0902 0.0000 4.5310 20.1072 1.0105
1 3 4 70.3730 45.0000 1.4731 0.0000 2.9000 0.0000 2.4464
3 3 3 77.3022 33.4558 1.4033 0.0000 3.9048 0.0000 1.0000
3 3 4 77.0669 27.6795 1.6466 0.0000 2.9000 0.0000 1.5085
4 3 4 68.8583 40.4712 1.8369 0.0000 3.0072 0.0000 1.5773
1 3 2 90.0000 34.3702 0.4674 0.0000 0.6101 0.0000 1.0013
2 3 3 90.0000 26.3185 8.0000 0.0000 0.8615 0.0000 1.0579
2 3 4 68.3253 36.1953 7.5000 0.0000 0.1000 0.0000 1.0000
2 3 2 80.7909 19.0967 1.0887 0.0000 2.0594 0.0000 1.7720
1 4 1 71.2077 14.1180 3.3944 0.0000 2.8702 0.0000 1.2651
1 4 3 76.1064 23.7583 1.6308 0.0000 2.8701 0.0000 1.6732
1 4 4 71.3624 12.8120 3.1458 0.0000 2.8701 0.0000 1.1896
3 4 3 74.2922 23.0742 2.6248 -18.0069 3.0701 0.0000 1.6278
3 4 4 74.0840 31.1381 1.5175 -0.9193 3.0117 0.0000 1.3541
4 4 4 76.0945 32.1176 1.7767 0.0000 2.9983 0.0000 1.9677
1 4 2 69.1892 14.8553 2.7174 0.0000 0.2025 0.0000 1.3071
2 4 3 74.5555 45.0000 1.1948 0.0000 0.3956 0.0000 3.0000
2 4 4 78.8758 45.0000 0.5964 0.0000 0.5437 0.0000 1.0000
2 4 2 81.5738 7.0792 7.5000 0.0000 0.1000 0.0000 1.0000
1 2 3 0.0000 21.4989 1.0000 0.0000 0.1000 0.0000 1.1358
1 2 4 0.0000 0.0100 2.4974 0.0000 0.0000 0.0000 1.3777
1 2 5 0.0000 15.0000 3.0000 0.0000 0.0000 0.0000 1.0400
3 2 3 0.0000 15.0000 0.5640 0.0000 0.0000 0.0000 1.0400
3 2 4 0.0000 1.0235 0.1000 0.0000 0.0000 0.0000 3.0000
4 2 4 0.0000 0.0100 1.3170 0.0000 0.0000 0.0000 2.1165
2 2 3 0.0000 2.0000 0.0839 0.0000 0.0000 0.0000 2.9374
2 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
1 1 5 74.4180 33.4273 1.7018 0.1463 0.5000 0.0000 1.6178
1 5 1 79.7037 28.2036 1.7073 0.1463 0.5000 0.0000 1.6453
2 1 5 63.3289 29.4225 2.1326 0.0000 0.5000 0.0000 3.0000
1 5 2 85.9449 38.3109 1.2492 0.0000 0.5000 0.0000 1.1000
1 5 5 85.6645 40.0000 2.9274 0.1463 0.5000 0.0000 1.3830
2 5 2 83.8555 5.1317 0.4377 0.0000 0.5000 0.0000 3.0000
2 5 5 97.0064 32.1121 2.0242 0.0000 0.5000 0.0000 2.8568
3 5 3 81.0926 30.2268 6.4132 -5.4471 2.5968 0.0000 3.0000
1 5 3 70.0000 35.0000 3.4223 0.0000 1.3550 0.0000 1.2002
1 3 5 57.3353 41.0012 1.0609 0.0000 1.3000 0.0000 3.0000
3 3 5 83.9753 31.0715 3.5590 0.0000 0.8161 0.0000 1.1776
2 3 5 89.8843 17.5000 3.3660 0.0000 2.0000 0.0000 2.0734
2 6 2 0.0000 49.8261 0.2093 0.0000 2.0870 0.0000 2.2895
2 2 6 0.0000 40.0366 3.1505 0.0000 1.1296 0.0000 1.1110
6 2 6 0.0000 0.5047 0.8000 0.0000 0.8933 0.0000 4.6650
2 6 6 0.0000 8.7037 0.0827 0.0000 3.5597 0.0000 1.1198
3 6 3 0.0000 9.2317 0.1000 0.0000 1.0000 0.0000 1.0920
6 3 6 0.0008 25.0000 8.0000 0.0000 1.0000 0.0000 3.0000
2 3 6 66.0423 5.0000 1.0000 0.0000 1.0000 0.0000 1.2500
2 6 3 0.0000 0.5000 0.1000 0.0000 1.0000 0.0000 3.0000
3 3 6 70.0000 20.0000 1.0000 0.0000 1.0000 0.0000 1.2500
3 7 3 90.0000 18.4167 0.6799 -8.0000 0.1310 0.0000 2.2321
2 3 7 72.6004 9.6150 0.8905 0.0000 3.5473 0.0000 1.0400
3 3 7 60.0000 40.0000 4.0000 0.0000 1.0000 0.0000 1.0400
3 2 7 0.0000 10.0000 1.0000 0.0000 1.0000 0.0000 1.0400
6 3 7 41.0995 3.2207 7.3523 0.0000 0.1101 0.0000 1.0947
7 3 7 62.1312 7.5931 0.1000 0.0000 0.5154 0.0000 2.1744
1 3 7 74.1394 8.5687 1.7132 0.0000 -0.6553 0.0000 2.2323
2 7 3 75.0000 25.0000 2.0000 0.0000 1.0000 0.0000 1.2500
3 7 7 70.0000 25.0000 2.0000 0.0000 1.0000 0.0000 1.2500
3 9 3 90.0000 30.4624 2.1468 0.0000 0.0500 0.0000 1.9485
9 3 9 90.0000 5.7486 5.0000 0.0000 2.0000 0.0000 1.1000
3 3 9 62.9344 15.0215 4.3743 0.0000 0.6168 0.0000 1.1673
3 9 9 33.7127 8.0623 3.4580 0.0000 0.0500 0.0000 2.6065
2 3 9 90.0000 9.7766 8.0000 0.0000 0.0505 0.0000 1.7257
1 3 9 90.0000 11.2108 1.4880 0.0000 0.5386 0.0000 2.1105
3 2 10 0.0000 0.0100 0.0100 0.0000 0.0000 0.0000 1.1456
11 1 11 77.8443 49.0744 5.9913 0.0000 0.7835 0.0000 2.3020
1 11 1 0.0000 19.9962 3.2299 0.0000 2.1012 0.0000 1.1537
1 11 11 0.0000 25.0000 1.0000 0.0000 1.0000 0.0000 1.0400
11 1 2 69.6421 10.0000 2.0000 0.0000 1.0000 0.0000 1.0400
4 9 4 90.0000 30.4624 2.1468 0.0000 0.0500 0.0000 1.9485
3 9 4 90.0000 30.4624 2.1468 0.0000 0.0500 0.0000 1.9485
9 4 9 90.0000 5.7486 5.0000 0.0000 2.0000 0.0000 1.1000
3 4 9 62.9344 15.0215 4.3743 0.0000 0.6168 0.0000 1.1673
4 3 9 62.9344 15.0215 4.3743 0.0000 0.6168 0.0000 1.1673
4 4 9 62.9344 15.0215 4.3743 0.0000 0.6168 0.0000 1.1673
4 4 9 62.9344 15.0215 4.3743 0.0000 0.6168 0.0000 1.1673
4 9 9 33.7127 8.0623 3.4580 0.0000 0.0500 0.0000 2.6065
2 4 9 90.0000 9.7766 8.0000 0.0000 0.0505 0.0000 1.7257
1 4 9 90.0000 11.2108 1.4880 0.0000 0.5386 0.0000 2.1105
3 12 3 90.0000 5.2360 6.0000 0.0000 1.9491 0.0000 1.0000
12 3 12 27.0723 4.9264 1.7778 0.0000 0.3851 0.0000 1.4855
2 3 12 1.0000 1.5989 6.0000 0.0000 0.6668 0.0000 1.0000
3 3 12 90.0000 10.0000 1.0000 0.0000 1.0000 0.0000 2.0000
1 3 12 70.0000 0.0000 1.0000 0.0000 1.0000 0.0000 2.0000
73 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n
1 1 1 1 0.0734 56.5103 0.0000 -5.5375 -2.6113 0.0000 0.0000
1 1 1 2 0.2335 44.4534 0.5000 -5.5234 -3.0000 0.0000 0.0000
2 1 1 2 -0.0100 59.3937 0.5000 -8.0000 -3.0000 0.0000 0.0000
1 1 1 3 -0.1605 9.1977 -1.0000 -2.5000 -2.1235 0.0000 0.0000
2 1 1 3 0.4631 41.1330 0.7425 -7.5125 -1.1040 0.0000 0.0000
3 1 1 3 -1.0000 30.3068 -1.0000 -8.5000 -0.0100 0.0000 0.0000
1 1 3 1 1.0000 45.3654 -0.7715 -3.2711 -0.0100 0.0000 0.0000
1 1 3 2 1.0000 150.0000 1.0000 -6.6407 -0.0100 0.0000 0.0000
2 1 3 1 1.0000 143.9644 0.6834 -6.1023 -1.1889 0.0000 0.0000
2 1 3 2 -1.0000 74.4134 1.0000 -3.3595 -3.5000 0.0000 0.0000
1 1 3 3 1.0000 133.2711 0.5065 -2.5561 -0.0100 0.0000 0.0000
2 1 3 3 0.2238 53.9090 0.8685 -2.7064 -3.5000 0.0000 0.0000
3 1 3 1 -1.0000 66.2620 0.7534 -3.3533 -2.2258 0.0000 0.0000
3 1 3 2 0.6489 19.7090 -1.0000 -3.3466 -0.1540 0.0000 0.0000
3 1 3 3 -1.0000 86.4981 1.0000 -3.5833 -0.0610 0.0000 0.0000
1 3 3 1 1.0000 0.1000 1.0000 -6.9024 -0.0100 0.0000 0.0000
1 3 3 2 0.9093 23.6198 -0.1431 -2.4750 -3.5000 0.0000 0.0000
2 3 3 2 -1.6122 5.0000 -1.0000 -2.5394 -0.9921 0.0000 0.0000
1 3 3 3 2.5000 2.1016 0.9647 -2.6000 -0.9972 0.0000 0.0000
2 3 3 3 -2.5000 75.7606 -0.6120 -7.8633 -1.2407 0.0000 0.0000
3 3 3 3 -0.5000 5.0000 1.0000 -2.5000 -0.9000 0.0000 0.0000
1 1 4 2 0.2700 43.1323 -0.4952 -7.6538 -1.9825 0.0000 0.0000
2 1 4 2 -0.5047 82.9784 0.8701 -7.6680 -2.1051 0.0000 0.0000
3 1 4 2 0.8306 15.5307 1.0000 -2.5000 -2.5261 0.0000 0.0000
3 1 1 4 -0.8051 19.8307 1.0000 -3.7979 -0.9511 0.0000 0.0000
4 1 1 4 1.0000 36.1913 1.0000 -3.4095 -1.7241 0.0000 0.0000
1 1 4 1 1.0000 32.6616 0.3481 -6.4524 -1.6589 0.0000 0.0000
3 1 4 1 -1.0000 -5.0000 1.0000 -2.5000 -1.8038 0.0000 0.0000
2 1 1 4 0.7529 50.8010 -0.5000 -4.3471 -1.9000 0.0000 0.0000
4 1 4 2 0.3787 13.7301 0.6579 -8.2500 -2.0202 0.0000 0.0000
2 1 4 1 -1.0000 76.7186 0.1194 -8.0000 -1.5996 0.0000 0.0000
0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
0 1 1 0 0.0000 60.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000
0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000
0 1 4 0 0.2176 40.4126 0.3535 -3.9875 -2.0051 0.0000 0.0000
0 2 4 0 0.0000 0.1032 0.3000 -5.0965 0.0000 0.0000 0.0000
0 3 4 0 1.1397 61.3225 0.5139 -3.8507 -2.7831 0.0000 0.0000
0 4 4 0 0.7265 44.3155 1.0000 -4.4046 -2.0000 0.0000 0.0000
4 1 4 4 -0.0949 8.7582 0.3310 -7.9430 -2.0000 0.0000 0.0000
0 1 5 0 4.0885 78.7058 0.1174 -2.1639 0.0000 0.0000 0.0000
0 5 5 0 -0.0170 -56.0786 0.6132 -2.2092 0.0000 0.0000 0.0000
0 2 5 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2 3 5 3 2.5000 2.5000 0.2237 -10.0000 -1.0000 0.0000 0.0000
0 3 5 0 -2.5000 50.0000 -0.5000 -10.0000 -1.0000 0.0000 0.0000
0 6 6 0 0.0000 0.0000 0.1200 -2.4426 0.0000 0.0000 0.0000
0 2 6 0 0.0000 0.0000 0.1200 -2.4847 0.0000 0.0000 0.0000
0 3 6 0 0.0000 0.0000 0.1200 -2.4703 0.0000 0.0000 0.0000
1 1 1 7 -0.3232 14.3871 0.1823 -9.8682 -1.7255 0.0000 0.0000
7 1 1 7 -0.1452 50.0000 -0.1915 -8.0773 -1.7255 0.0000 0.0000
0 1 7 0 4.0000 45.8264 0.9000 -4.0000 0.0000 0.0000 0.0000
0 7 7 0 4.0000 45.8264 0.9000 -4.0000 0.0000 0.0000 0.0000
2 1 3 7 -1.5000 18.9285 0.3649 -6.1208 0.0000 0.0000 0.0000
2 3 7 3 1.5000 -1.0000 0.2575 -6.2100 0.0000 0.0000 0.0000
1 3 7 3 -1.4375 -0.8700 0.9861 -2.5424 0.0000 0.0000 0.0000
7 3 7 3 -1.5000 21.5086 -1.0000 -4.8869 0.0000 0.0000 0.0000
2 1 3 9 0.1714 69.9743 0.9170 -7.9557 0.0000 0.0000 0.0000
1 1 3 9 0.2500 76.5218 1.0000 -2.5503 0.0000 0.0000 0.0000
3 1 3 9 -0.2500 50.5929 -0.2500 -6.9285 0.0000 0.0000 0.0000
2 3 9 3 -0.2500 0.0100 -0.5000 -4.6984 0.0000 0.0000 0.0000
1 1 1 11 0.5000 0.1000 0.4683 -11.5274 -1.7255 0.0000 0.0000
2 1 1 11 0.0000 49.3871 0.2000 -10.5765 -1.7255 0.0000 0.0000
11 1 1 11 -0.5000 95.4727 -0.2080 -4.8579 -1.7255 0.0000 0.0000
0 1 11 0 4.0000 45.8264 0.9000 -4.0000 0.0000 0.0000 0.0000
0 11 11 0 4.0000 45.8264 0.8897 -4.0000 0.0000 0.0000 0.0000
2 1 4 9 0.1714 69.9743 0.9170 -7.9557 0.0000 0.0000 0.0000
1 1 4 9 0.2500 76.5218 1.0000 -2.5503 0.0000 0.0000 0.0000
3 1 4 9 -0.2500 50.5929 -0.2500 -6.9285 0.0000 0.0000 0.0000
4 1 4 9 -0.2500 50.5929 -0.2500 -6.9285 0.0000 0.0000 0.0000
4 1 3 9 -0.2500 50.5929 -0.2500 -6.9285 0.0000 0.0000 0.0000
2 4 9 3 -0.2500 0.0100 -0.5000 -4.6984 0.0000 0.0000 0.0000
2 4 9 4 -0.2500 0.0100 -0.5000 -4.6984 0.0000 0.0000 0.0000
0 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1
data/benchmarks/water/ffield_acks2.water 0 → 100644
+ 364
− 0
View file @ 70d872fe
Reactive MD-force field: Water
39 ! Number of general parameters
50.0000 !Overcoordination parameter
9.5469 !Overcoordination parameter
26.5405 !Valency angle conjugation parameter
1.7224 !Triple bond stabilisation parameter
6.8702 !Triple bond stabilisation parameter
60.4850 !C2-correction
1.0588 !Undercoordination parameter
4.6000 !Triple bond stabilisation parameter
12.1176 !Undercoordination parameter
13.3056 !Undercoordination parameter
-70.5044 !Triple bond stabilization energy
0.0000 !Lower Taper-radius
10.0000 !Upper Taper-radius
2.8793 !Not used
33.8667 !Valency undercoordination
6.0891 !Valency angle/lone pair parameter
1.0563 !Valency angle
2.0384 !Valency angle parameter
6.1431 !Not used
6.9290 !Double bond/angle parameter
0.3989 !Double bond/angle parameter: overcoord
3.9954 !Double bond/angle parameter: overcoord
-2.4837 !Not used
5.7796 !Torsion/BO parameter
10.0000 !Torsion overcoordination
1.9487 !Torsion overcoordination
-1.2327 !Conjugation 0 (not used)
2.1645 !Conjugation
1.5591 !vdWaals shielding
0.1000 !Cutoff for bond order (*100)
2.1365 !Valency angle conjugation parameter
0.6991 !Overcoordination parameter
50.0000 !Overcoordination parameter
1.8512 !Valency/lone pair parameter
548.6451 !Softness
20.0000 !Not used
5.0000 !Molecular energy (not used)
0.0000 !Molecular energy (not used)
2.6962 !Valency angle conjugation parameter
15 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;#
alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u.
cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u.
ov/un;val1;n.u.;val3,vval4
C 1.3817 4.0000 12.0000 1.8903 0.1838 0.9000 1.1341 4.0000
9.7559 2.1346 4.0000 34.9350 79.5548 5.9666 7.0000 0.0000
1.2114 0.0000 202.5551 8.9539 34.9289 13.5366 0.8563 0.0000
-2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000
H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000
8.2230 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000
-0.1000 0.0000 61.6606 3.0408 2.4197 0.0003 3.4114 0.0000
-19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000
O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000
9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000
0.9049 0.4056 59.0626 3.5027 0.7640 0.0021 0.9745 0.0000
-3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000
N 1.2333 3.0000 14.0000 1.9324 0.1376 0.8596 1.1748 5.0000
10.0667 7.8431 4.0000 32.2482 100.0000 6.8418 6.3404 2.0000
1.0433 13.7673 119.9837 2.1961 3.0696 2.7683 0.9745 0.0000
-4.3875 2.6192 1.0183 4.0000 2.8793 0.0000 0.0000 0.0000
S 1.9405 2.0000 32.0600 2.0677 0.2099 1.0336 1.5479 6.0000
9.9575 4.9055 4.0000 52.9998 112.1416 6.5000 8.2545 2.0000
1.4601 9.7177 71.1843 5.7487 23.2859 12.7147 0.9745 0.0000
-11.0000 2.7466 1.0338 6.2998 2.8793 0.0000 0.0000 0.0000
Si 2.0276 4.0000 28.0600 2.2042 0.1322 0.8218 1.5758 4.0000
11.9413 2.0618 4.0000 11.8211 136.4845 1.8038 7.3852 0.0000
-1.0000 0.0000 126.5182 6.4918 8.5961 0.2368 0.8563 0.0000
-3.8112 3.1873 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
Pt 1.9907 3.0000 195.0800 1.9980 0.2452 0.8218 -1.0000 3.0000
12.8669 3.2118 3.0000 0.0000 0.0000 1.8038 7.3852 0.0000
-1.0000 0.0000 142.6300 6.2293 5.2294 0.1542 0.8563 0.0000
-6.7740 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
Zr 2.1000 4.0000 91.2240 2.1970 0.2542 0.8218 -1.0000 4.0000
12.8545 3.5938 4.0000 0.0000 0.0000 1.8038 7.3852 0.0000
-1.0000 0.0000 107.6300 6.2293 5.2294 0.1542 0.8563 0.0000
-3.2224 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
Ni 1.8503 2.0000 58.6900 1.9219 0.1582 0.8218 -1.0000 2.0000
12.1238 4.0351 2.0000 0.0000 0.0000 1.8038 7.3852 0.0000
-1.0000 0.0000 95.6300 6.2293 5.2294 0.1542 0.8563 0.0000
-3.2224 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
Au 1.8503 1.0000 196.9665 1.9219 0.1582 0.8218 -1.0000 1.0000
12.1238 4.0351 1.0000 0.0000 0.0000 1.8038 7.3852 0.0000
-1.0000 0.0000 72.6300 6.2293 5.2294 0.1542 0.8563 0.0000
-3.2224 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
V 2.2657 3.0000 50.9415 1.7992 0.3005 0.6743 0.1000 5.0000
12.3879 5.2243 3.0000 0.0000 0.0000 -0.3628 6.6023 0.0000
-1.0000 0.0000 117.6300 23.1946 6.5795 0.0000 0.8563 0.0000
-3.5389 1.5012 1.0338 3.0000 3.6411 0.0000 0.0000 0.0000
Bi 2.1949 3.0000 208.9804 2.4429 0.1607 0.4960 0.0535 5.0000
12.9571 35.5167 3.0000 0.0000 0.0000 -0.1926 6.4153 0.0000
-1.0000 0.5785 52.6300 3.8978 0.9856 0.0314 0.8563 0.0000
-2.5000 5.0597 1.0338 6.0000 2.5791 0.0000 0.0000 0.0000
Ti 0.1000 4.0000 47.8800 2.0000 0.1659 0.6037 0.1000 4.0000
13.2535 4.0063 4.0000 -5.0000 0.0000 -0.1864 5.9304 0.0000
-1.0000 0.0000 129.6300 22.8461 1.8515 0.0064 0.8563 0.0000
-3.4122 3.2711 1.0338 6.2998 2.2632 0.0000 0.0000 0.0000
Mo 2.4710 5.6504 95.9400 1.8000 0.3285 1.0000 0.1000 6.0000
13.0000 45.0000 4.0000 0.0000 0.0000 0.6062 6.1484 0.0000
0.1000 0.0000 152.6300 3.7659 0.0689 2.9902 0.8563 0.0000
-16.7660 3.1072 1.0338 8.0000 3.4590 0.0000 0.0000 0.0000
X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000
10.0000 2.5000 4.0000 0.0000 0.0000 8.5000 1.5000 0.0000
-0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.9745 0.0000
-11.0000 2.7466 1.0338 2.0000 2.8793 0.0000 0.0000 0.0000
40 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6
pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr
1 1 158.2004 99.1897 78.0000 -0.7738 -0.4550 1.0000 37.6117 0.4147
0.4590 -0.1000 9.1628 1.0000 -0.0777 6.7268 1.0000 0.0000
1 2 169.4760 0.0000 0.0000 -0.6083 0.0000 1.0000 6.0000 0.7652
5.2290 1.0000 0.0000 1.0000 -0.0500 6.9136 0.0000 0.0000
2 2 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300
6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000
1 3 158.6946 107.4583 23.3136 -0.4240 -0.1743 1.0000 10.8209 1.0000
0.5322 -0.3113 7.0000 1.0000 -0.1447 5.2450 0.0000 0.0000
3 3 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051
0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000
1 4 134.1215 140.2179 79.9745 0.0163 -0.1428 1.0000 27.0617 0.2000
0.1387 -0.3681 7.1611 1.0000 -0.1000 5.0825 1.0000 0.0000
3 4 130.8596 169.4551 40.0000 0.3837 -0.1639 1.0000 35.0000 0.2000
1.0000 -0.3579 7.0004 1.0000 -0.1193 6.8773 1.0000 0.0000
4 4 157.9384 82.5526 152.5336 0.4010 -0.1034 1.0000 12.4261 0.5828
0.1578 -0.1509 11.9186 1.0000 -0.0861 5.4271 1.0000 0.0000
2 3 160.0000 0.0000 0.0000 -0.5725 0.0000 1.0000 6.0000 0.5626
1.1150 1.0000 0.0000 0.0000 -0.0920 4.2790 0.0000 0.0000
2 4 231.8173 0.0000 0.0000 -0.3364 0.0000 1.0000 6.0000 0.4402
8.8910 1.0000 0.0000 1.0000 -0.0327 6.5754 0.0000 0.0000
1 5 128.9942 74.5848 55.2528 0.1035 -0.5211 1.0000 18.9617 0.6000
0.2949 -0.2398 8.1175 1.0000 -0.1029 5.6731 1.0000 0.0000
2 5 151.5159 0.0000 0.0000 -0.4721 0.0000 1.0000 6.0000 0.6000
9.4366 1.0000 0.0000 1.0000 -0.0290 7.0050 1.0000 0.0000
3 5 0.0000 0.0000 0.0000 0.5563 -0.4038 1.0000 49.5611 0.6000
0.4259 -0.4577 12.7569 1.0000 -0.1100 7.1145 1.0000 0.0000
4 5 0.0000 0.0000 0.0000 0.4438 -0.2034 1.0000 40.3399 0.6000
0.3296 -0.3153 9.1227 1.0000 -0.1805 5.6864 1.0000 0.0000
5 5 96.1871 93.7006 68.6860 0.0955 -0.4781 1.0000 17.8574 0.6000
0.2723 -0.2373 9.7875 1.0000 -0.0950 6.4757 1.0000 0.0000
6 6 109.1904 70.8314 30.0000 0.2765 -0.3000 1.0000 16.0000 0.1583
0.2804 -0.1994 8.1117 1.0000 -0.0675 8.2993 0.0000 0.0000
2 6 137.1002 0.0000 0.0000 -0.1902 0.0000 1.0000 6.0000 0.4256
17.7186 1.0000 0.0000 1.0000 -0.0377 6.4281 0.0000 0.0000
3 6 191.1743 52.0733 43.3991 -0.2584 -0.3000 1.0000 36.0000 0.8764
1.0248 -0.3658 4.2151 1.0000 -0.5004 4.2605 1.0000 0.0000
4 6 185.4488 39.2832 43.3991 -0.1922 -0.3000 1.0000 36.0000 0.8217
0.8538 -0.3887 4.4334 1.0000 -0.5241 4.4529 1.0000 0.0000
7 7 90.1462 0.0000 0.0000 0.0004 -0.2000 0.0000 16.0000 0.3484
1.0000 -0.2000 15.0000 1.0000 -0.1014 5.7631 0.0000 0.0000
8 8 85.2900 0.0000 0.0000 0.0004 -0.2000 0.0000 16.0000 0.5438
1.0000 -0.2000 15.0000 1.0000 -0.1001 5.5699 0.0000 0.0000
9 9 73.6182 0.0000 0.0000 0.0004 -0.2000 0.0000 16.0000 0.3418
1.0000 -0.2000 15.0000 1.0000 -0.1015 5.7850 0.0000 0.0000
10 10 73.6182 0.0000 0.0000 0.0004 -0.2000 0.0000 16.0000 0.3418
1.0000 -0.2000 15.0000 1.0000 -0.1015 5.7850 0.0000 0.0000
11 11 36.2751 0.0000 0.0000 0.8059 -0.3000 0.0000 16.0000 0.1826
0.3414 -0.3000 16.0000 1.0000 -0.0717 7.9108 0.0000 0.0000
3 11 106.8008 67.5543 0.0000 0.0323 -0.3000 1.0000 36.0000 0.1000
0.2670 -0.3402 16.0000 1.0000 -0.1761 4.6698 1.0000 0.0000
2 11 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
1 11 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
12 12 66.0677 0.0000 0.0000 -0.9557 -0.2000 0.0000 16.0000 0.2865
0.5847 -0.2000 15.0000 1.0000 -0.0856 5.2857 0.0000 0.0000
3 12 152.2407 57.6204 0.0000 -0.8033 -0.3000 1.0000 36.0000 0.0498
1.8097 -0.3800 16.0000 1.0000 -0.2379 8.0000 1.0000 0.0000
2 12 95.9209 0.0000 0.0000 -0.0153 -0.3000 1.0000 36.0000 0.0100
1.0000 -0.2062 8.6647 1.0000 -0.1911 4.0000 1.0000 0.0000
1 12 78.9091 40.6322 0.0000 0.0040 -0.3000 1.0000 36.0000 0.0384
0.0904 -0.1209 12.3682 1.0000 -0.1613 4.3849 1.0000 0.0000
13 13 71.3016 10.0000 0.0000 -0.1571 -0.2000 0.0000 16.0000 0.3311
0.1822 -0.2000 15.0000 1.0000 -0.1860 6.5172 0.0000 0.0000
3 13 112.7130 29.8084 0.0000 -0.9010 -0.3000 1.0000 36.0000 0.5508
0.1006 -0.2492 16.9476 1.0000 -0.1919 5.4797 1.0000 0.0000
1 13 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
2 13 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
1 14 0.5356 0.9614 0.0000 0.3817 -0.3000 1.0000 36.0000 0.2142
0.6116 -0.2579 6.1366 1.0000 -0.0913 6.6008 1.0000 0.0000
2 14 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.3027 4.6243 1.0000 -0.4578 3.5219 1.0000 0.0000
3 14 112.7070 10.0000 135.5011 0.9277 -0.2354 1.0000 19.1731 1.2334
0.9822 -0.1837 7.2216 1.0000 -0.1264 6.1257 1.0000 0.0000
14 14 44.6382 0.0000 0.0000 1.0000 -0.3000 0.0000 16.0000 0.2890
0.3384 -0.3000 16.0000 1.0000 -0.1862 7.4588 0.0000 0.0000
12 14 50.0000 0.0000 0.0000 0.1000 -0.3000 0.0000 16.0000 0.3000
1.0000 -0.3000 16.0000 1.0000 -0.2000 8.0000 0.0000 0.0000
20 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2
1 2 0.1239 1.4004 9.8467 1.1210 -1.0000 -1.0000
2 3 0.0283 1.2885 10.9190 0.9215 -1.0000 -1.0000
2 4 0.1059 1.8290 9.7818 0.9598 -1.0000 -1.0000
1 3 0.1156 1.8520 9.8317 1.2854 1.1352 1.0706
1 4 0.1447 1.8766 9.7990 1.3436 1.1885 1.1363
3 4 0.1048 2.0003 10.1220 1.3173 1.1096 1.0206
2 6 0.0470 1.6738 11.6877 1.1931 -1.0000 -1.0000
3 6 0.1263 1.8163 10.6833 1.6266 1.2052 -1.0000
1 11 0.1995 2.2133 13.0000 0.0102 1.4868 -1.0000
2 11 0.1319 1.5855 12.5457 0.0099 1.5065 -1.0000
3 11 0.0813 1.8649 10.8791 1.6498 1.6445 -1.0000
1 12 0.4235 1.7716 11.3664 1.8000 1.7212 -1.0000
2 12 0.0754 1.6033 12.4204 1.6896 -1.5000 -1.0000
3 12 0.1648 2.1260 11.2425 2.0692 1.6939 -1.0000
2 13 0.1340 1.8546 11.5784 1.0000 -1.0000 -1.0000
3 13 0.1280 1.8000 10.5743 1.7358 1.5296 -1.0000
1 13 0.1301 1.9382 11.1255 0.0100 -1.0000 -1.0000
1 14 0.1495 2.0794 12.2376 0.0100 1.4060 -1.0000
2 14 0.0795 1.6794 11.2376 0.0100 1.2060 -1.0000
3 14 0.2101 2.0342 10.4729 1.6019 1.4781 1.6548
97 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2
1 1 1 59.0573 30.7029 0.7606 0.0000 0.7180 6.2933 1.1244
1 1 2 65.7758 14.5234 6.2481 0.0000 0.5665 0.0000 1.6255
2 1 2 70.2607 25.2202 3.7312 0.0000 0.0050 0.0000 2.7500
1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400
1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400
2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400
1 1 3 49.6811 7.1713 4.3889 0.0000 0.7171 10.2661 1.0463
3 1 3 77.7473 40.1718 2.9802 -25.3063 1.6170 -46.1315 2.2503
1 1 4 66.1305 12.4661 7.0000 0.0000 3.0000 50.0000 1.1880
3 1 4 73.9544 12.4661 7.0000 0.0000 3.0000 0.0000 1.1880
4 1 4 64.1581 12.4661 7.0000 0.0000 3.0000 0.0000 1.1880
2 1 3 65.0000 13.8815 5.0583 0.0000 0.4985 0.0000 1.4900
2 1 4 74.2929 31.0883 2.6184 0.0000 0.0755 0.0000 1.0500
1 2 4 0.0000 0.0019 6.3000 0.0000 0.0000 0.0000 1.0400
1 3 1 73.5312 44.7275 0.7354 0.0000 3.0000 0.0000 1.0684
1 3 3 79.4761 36.3701 1.8943 0.0000 0.7351 67.6777 3.0000
1 3 4 82.4890 31.4554 0.9953 0.0000 1.6310 0.0000 1.0783
3 3 3 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783
3 3 4 84.3637 31.4554 0.9953 0.0000 1.6310 0.0000 1.0783
4 3 4 89.7071 31.4554 0.9953 0.0000 1.6310 0.0000 1.1519
1 3 2 70.1880 20.9562 0.3864 0.0000 0.0050 0.0000 1.6924
2 3 3 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680
2 3 4 75.6201 18.7919 0.9833 0.0000 0.1218 0.0000 1.0500
2 3 2 85.8000 9.8453 2.2720 0.0000 2.8635 0.0000 1.5800
1 4 1 66.0330 22.0295 1.4442 0.0000 1.6777 0.0000 1.0500
1 4 3 103.3204 33.0381 0.5787 0.0000 1.6777 0.0000 1.0500
1 4 4 104.1335 8.6043 1.6495 0.0000 1.6777 0.0000 1.0500
3 4 3 74.1978 42.1786 1.7845 -18.0069 1.6777 0.0000 1.0500
3 4 4 74.8600 43.7354 1.1572 -0.9193 1.6777 0.0000 1.0500
4 4 4 75.0538 14.8267 5.2794 0.0000 1.6777 0.0000 1.0500
1 4 2 69.1106 25.5067 1.1003 0.0000 0.0222 0.0000 1.0369
2 4 3 81.3686 40.0712 2.2396 0.0000 0.0222 0.0000 1.0369
2 4 4 83.0104 43.4766 1.5328 0.0000 0.0222 0.0000 1.0500
2 4 2 70.8687 12.0168 5.0132 0.0000 0.0222 0.0000 1.1243
1 2 3 0.0000 25.0000 3.0000 0.0000 1.0000 0.0000 1.0400
1 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
1 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
3 2 3 0.0000 15.0000 2.8900 0.0000 0.0000 0.0000 2.8774
3 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
4 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
2 2 3 0.0000 8.5744 3.0000 0.0000 0.0000 0.0000 1.0421
2 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
1 1 5 74.9397 25.0560 1.8787 0.1463 0.0559 0.0000 1.0400
1 5 1 86.9521 36.9951 2.0903 0.1463 0.0559 0.0000 1.0400
2 1 5 74.9397 25.0560 1.8787 0.0000 0.0000 0.0000 1.0400
1 5 2 86.1791 36.9951 2.0903 0.0000 0.0000 0.0000 1.0400
1 5 5 85.3644 36.9951 2.0903 0.1463 0.0559 0.0000 1.0400
2 5 2 93.1959 36.9951 2.0903 0.0000 0.0000 0.0000 1.0400
2 5 5 84.3331 36.9951 2.0903 0.0000 0.0000 0.0000 1.0400
6 6 6 69.3456 21.7361 1.4283 0.0000 -0.2101 0.0000 1.3241
2 6 6 75.6168 21.5317 1.0435 0.0000 2.5179 0.0000 1.0400
2 6 2 78.3939 20.9772 0.8630 0.0000 2.8421 0.0000 1.0400
3 6 6 70.3016 15.4081 1.3267 0.0000 2.1459 0.0000 1.0400
2 6 3 73.8232 16.6592 3.7425 0.0000 0.8613 0.0000 1.0400
3 6 3 90.0344 7.7656 1.7264 0.0000 0.7689 0.0000 1.0400
6 3 6 22.1715 3.6615 0.3160 0.0000 4.1125 0.0000 1.0400
2 3 6 83.7634 5.6693 2.7780 0.0000 1.6982 0.0000 1.0400
3 3 6 73.4663 25.0761 0.9143 0.0000 2.2466 0.0000 1.0400
2 2 6 0.0000 47.1300 6.0000 0.0000 1.6371 0.0000 1.0400
6 2 6 0.0000 31.5209 6.0000 0.0000 1.6371 0.0000 1.0400
3 2 6 0.0000 31.0427 4.5625 0.0000 1.6371 0.0000 1.0400
2 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
3 11 3 62.4906 31.5023 1.3328 0.0000 2.8731 0.0000 1.0794
11 3 11 31.0790 19.3435 0.4919 0.0000 2.9625 0.0000 3.0000
3 3 11 100.0000 14.7642 7.0000 0.0000 1.0585 0.0000 1.1599
1 3 11 60.7895 13.6681 0.7546 0.0000 2.1747 0.0000 2.9508
2 3 11 100.0000 5.0000 1.4335 0.0000 1.2363 0.0000 5.0000
3 12 12 23.8296 8.9089 7.0000 0.0000 1.0000 0.0000 2.8891
3 12 3 87.0764 19.4489 2.5080 0.0000 2.6056 0.0000 3.0000
12 3 12 72.7369 13.7522 5.0243 0.0000 2.9700 0.0000 1.5506
3 3 12 68.8771 10.5000 2.5500 0.0000 2.5729 0.0000 1.5892
2 3 12 99.5836 5.4142 2.2105 0.0000 1.0513 0.0000 1.1000
1 3 12 90.0000 12.1772 2.2055 0.0000 1.9064 0.0000 2.6056
1 1 12 71.1708 32.6379 0.4516 0.0000 2.1609 0.0000 1.1000
1 12 3 90.0000 45.0000 0.9335 0.0000 0.2140 0.0000 1.4846
1 12 1 87.6204 45.0000 1.2740 0.0000 1.1519 0.0000 1.1000
3 1 12 54.7020 3.2967 7.0000 0.0000 2.0408 0.0000 2.4032
2 12 3 90.0000 28.2099 1.8036 0.0000 1.5461 0.0000 1.2304
2 12 2 90.0000 36.3001 0.6409 0.0000 3.0000 0.0000 1.7755
1 12 2 89.5835 45.0000 0.8465 0.0000 1.2118 0.0000 2.2282
2 1 12 68.7714 22.9669 0.4631 0.0000 2.4269 0.0000 1.4680
2 2 12 0.0000 30.2898 3.9181 0.0000 0.9914 0.0000 1.3121
3 2 12 0.0000 1.0000 4.1706 0.0000 1.0100 0.0000 1.1000
1 2 12 0.0000 1.0000 3.9722 0.0000 1.0075 0.0000 1.2984
3 13 3 73.6321 10.6453 2.7693 0.0000 0.0500 0.0000 1.9906
13 3 13 100.0000 5.0270 5.0000 0.0000 1.2768 0.0000 2.0630
3 3 13 52.3127 40.0000 1.1362 0.0000 1.5100 0.0000 1.1000
3 13 13 66.6695 0.0036 3.2646 0.0000 0.0581 0.0000 1.3741
2 3 13 100.0000 3.8927 8.0000 0.0000 2.0000 0.0000 1.1000
1 3 13 96.6040 9.4537 8.0000 0.0000 0.3285 0.0000 4.0000
3 14 3 79.6765 50.0000 1.0502 -0.0016 0.1000 0.0000 1.4583
14 3 14 20.2100 37.6165 0.6059 0.0000 0.1531 0.0000 2.0586
3 3 14 38.5570 11.9307 0.9911 0.0000 0.8422 0.0000 1.0500
3 14 14 5.8342 0.0724 0.1000 0.0000 0.5490 0.0000 1.7839
2 3 14 81.8943 7.2820 2.1490 0.0000 0.6873 0.0000 3.2184
1 3 14 75.5634 8.3289 1.0236 0.0000 2.0875 0.0000 1.0500
12 3 14 30.0000 5.0000 0.5000 0.0000 0.5000 0.0000 1.2500
47 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n
1 1 1 1 -0.2500 34.7453 0.0288 -6.3507 -1.6000 0.0000 0.0000
1 1 1 2 -0.2500 29.2131 0.2945 -4.9581 -2.1802 0.0000 0.0000
2 1 1 2 -0.2500 31.2081 0.4539 -4.8923 -2.2677 0.0000 0.0000
1 1 1 3 -0.3495 22.2142 -0.2959 -2.5000 -1.9066 0.0000 0.0000
2 1 1 3 0.0646 24.3195 0.6259 -3.9603 -1.0000 0.0000 0.0000
3 1 1 3 -0.5456 5.5756 0.8433 -5.1924 -1.0180 0.0000 0.0000
1 1 3 1 1.7555 27.9267 0.0072 -2.6533 -1.0000 0.0000 0.0000
1 1 3 2 -1.4358 36.7830 -1.0000 -8.1821 -1.0000 0.0000 0.0000
2 1 3 1 -1.3959 34.5053 0.7200 -2.5714 -2.1641 0.0000 0.0000
2 1 3 2 -2.5000 70.0597 1.0000 -3.5539 -2.9929 0.0000 0.0000
1 1 3 3 0.6852 11.2819 -0.4784 -2.5000 -2.1085 0.0000 0.0000
2 1 3 3 0.1933 80.0000 1.0000 -4.0590 -3.0000 0.0000 0.0000
3 1 3 1 -1.9889 76.4820 -0.1796 -3.8301 -3.0000 0.0000 0.0000
3 1 3 2 0.2160 72.7707 -0.7087 -4.2100 -3.0000 0.0000 0.0000
3 1 3 3 -2.5000 71.0772 0.2542 -3.1631 -3.0000 0.0000 0.0000
1 3 3 1 2.5000 -0.6002 1.0000 -3.4297 -2.8858 0.0000 0.0000
1 3 3 2 -2.5000 -3.3822 0.7004 -5.4467 -2.9586 0.0000 0.0000
2 3 3 2 2.5000 -4.0000 0.9000 -2.5000 -1.0000 0.0000 0.0000
1 3 3 3 1.2329 -4.0000 1.0000 -2.5000 -1.7479 0.0000 0.0000
2 3 3 3 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 0.0000 0.0000
3 3 3 3 -2.5000 -4.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000
0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000
0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000
0 1 4 0 -2.4242 128.1636 0.3739 -6.6098 -2.0000 0.0000 0.0000
0 2 4 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
0 3 4 0 1.4816 55.6641 0.0004 -7.0465 -2.7203 0.0000 0.0000
0 4 4 0 -0.3244 27.7086 0.0039 -2.8272 -2.0000 0.0000 0.0000
4 1 4 4 -5.5181 8.9706 0.0004 -6.1782 -2.0000 0.0000 0.0000
0 1 5 0 3.3423 30.3435 0.0365 -2.7171 0.0000 0.0000 0.0000
0 5 5 0 -0.0555 -42.7738 0.1515 -2.2056 0.0000 0.0000 0.0000
0 2 5 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 6 6 0 0.0000 0.0000 0.1200 -2.4426 0.0000 0.0000 0.0000
0 2 6 0 0.0000 0.0000 0.1200 -2.4847 0.0000 0.0000 0.0000
0 3 6 0 0.0000 0.0000 0.1200 -2.4703 0.0000 0.0000 0.0000
2 1 3 14 1.6297 56.8132 0.3398 -2.6912 -2.1000 0.0000 0.0000
1 1 3 14 -0.0427 13.4096 0.9351 -6.5245 -2.1000 0.0000 0.0000
2 3 14 3 2.5000 11.6208 1.0000 -9.0000 -1.0000 0.0000 0.0000
2 1 3 12 -0.2500 45.7639 0.3000 -3.5745 -2.1565 0.0000 0.0000
1 1 3 12 -0.2500 69.1094 0.3000 -3.0983 -2.1565 0.0000 0.0000
2 3 12 3 -0.4306 7.5000 -0.5000 -6.9948 -1.0000 0.0000 0.0000
2 3 11 3 1.8627 9.7180 -1.0000 -7.2224 -1.0000 0.0000 0.0000
1 3 11 3 2.5000 23.9443 1.0000 -3.2267 -1.0000 0.0000 0.0000
1 1 3 11 0.9114 62.5039 -0.2389 -3.2976 -1.0000 0.0000 0.0000
2 1 3 11 0.5000 35.0000 0.5000 -4.0000 -1.0000 0.0000 0.0000
9 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1
3 2 3 2.1200 -3.5800 1.4500 19.5000
3 2 4 2.0000 -6.0000 1.7976 3.0000
4 2 3 1.2000 -2.0000 1.7976 3.0000
4 2 4 1.2979 -6.0000 1.7976 3.0000
3 2 5 1.5000 -2.0000 1.7976 3.0000
4 2 5 1.5000 -2.0000 1.7976 3.0000
5 2 3 1.5000 -2.0000 1.7976 3.0000
5 2 4 1.5000 -2.0000 1.7976 3.0000
5 2 5 1.5000 -2.0000 1.7976 3.0000
data/benchmarks/water/ffield_acks2_300.water 0 → 100644
+ 364
− 0
View file @ 70d872fe
Reactive MD-force field: Water
39 ! Number of general parameters
50.0000 !Overcoordination parameter
9.5469 !Overcoordination parameter
26.5405 !Valency angle conjugation parameter
1.7224 !Triple bond stabilisation parameter
6.8702 !Triple bond stabilisation parameter
60.4850 !C2-correction
1.0588 !Undercoordination parameter
4.6000 !Triple bond stabilisation parameter
12.1176 !Undercoordination parameter
13.3056 !Undercoordination parameter
-70.5044 !Triple bond stabilization energy
0.0000 !Lower Taper-radius
10.0000 !Upper Taper-radius
2.8793 !Not used
33.8667 !Valency undercoordination
6.0891 !Valency angle/lone pair parameter
1.0563 !Valency angle
2.0384 !Valency angle parameter
6.1431 !Not used
6.9290 !Double bond/angle parameter
0.3989 !Double bond/angle parameter: overcoord
3.9954 !Double bond/angle parameter: overcoord
-2.4837 !Not used
5.7796 !Torsion/BO parameter
10.0000 !Torsion overcoordination
1.9487 !Torsion overcoordination
-1.2327 !Conjugation 0 (not used)
2.1645 !Conjugation
1.5591 !vdWaals shielding
0.1000 !Cutoff for bond order (*100)
2.1365 !Valency angle conjugation parameter
0.6991 !Overcoordination parameter
50.0000 !Overcoordination parameter
1.8512 !Valency/lone pair parameter
548.6451 !Softness
20.0000 !Not used
5.0000 !Molecular energy (not used)
0.0000 !Molecular energy (not used)
2.6962 !Valency angle conjugation parameter
15 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;#
alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u.
cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u.
ov/un;val1;n.u.;val3,vval4
C 1.3817 4.0000 12.0000 1.8903 0.1838 0.9000 1.1341 4.0000
9.7559 2.1346 4.0000 34.9350 79.5548 5.9666 7.0000 0.0000
1.2114 0.0000 202.5551 8.9539 34.9289 13.5366 0.8563 0.0000
-2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000
H 0.8873 1.0000 1.0080 1.5420 0.0598 0.6883 -0.1000 1.0000
8.1910 30.9706 1.0000 0.0000 121.1250 3.5768 10.5896 1.0000
-0.1000 0.0000 61.6606 1.3986 2.1457 0.0003 3.4114 0.0000
-15.7683 2.1488 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000
O 1.2450 2.0000 15.9990 2.3878 0.1023 1.0903 1.0548 6.0000
10.5750 32.3923 4.0000 37.5000 116.0768 8.5000 7.5600 2.0000
0.9049 -1.0100 59.0626 2.7162 3.2532 0.0021 0.9745 0.0000
-3.6141 2.7025 1.0493 4.0000 2.9225 0.0000 5.4479 0.0000
N 1.2333 3.0000 14.0000 1.9324 0.1376 0.8596 1.1748 5.0000
10.0667 7.8431 4.0000 32.2482 100.0000 6.8418 6.3404 2.0000
1.0433 13.7673 119.9837 2.1961 3.0696 2.7683 0.9745 0.0000
-4.3875 2.6192 1.0183 4.0000 2.8793 0.0000 0.0000 0.0000
S 1.9405 2.0000 32.0600 2.0677 0.2099 1.0336 1.5479 6.0000
9.9575 4.9055 4.0000 52.9998 112.1416 6.5000 8.2545 2.0000
1.4601 9.7177 71.1843 5.7487 23.2859 12.7147 0.9745 0.0000
-11.0000 2.7466 1.0338 6.2998 2.8793 0.0000 0.0000 0.0000
Si 2.0276 4.0000 28.0600 2.2042 0.1322 0.8218 1.5758 4.0000
11.9413 2.0618 4.0000 11.8211 136.4845 1.8038 7.3852 0.0000
-1.0000 0.0000 126.5182 6.4918 8.5961 0.2368 0.8563 0.0000
-3.8112 3.1873 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
Pt 1.9907 3.0000 195.0800 1.9980 0.2452 0.8218 -1.0000 3.0000
12.8669 3.2118 3.0000 0.0000 0.0000 1.8038 7.3852 0.0000
-1.0000 0.0000 142.6300 6.2293 5.2294 0.1542 0.8563 0.0000
-6.7740 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
Zr 2.1000 4.0000 91.2240 2.1970 0.2542 0.8218 -1.0000 4.0000
12.8545 3.5938 4.0000 0.0000 0.0000 1.8038 7.3852 0.0000
-1.0000 0.0000 107.6300 6.2293 5.2294 0.1542 0.8563 0.0000
-3.2224 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
Ni 1.8503 2.0000 58.6900 1.9219 0.1582 0.8218 -1.0000 2.0000
12.1238 4.0351 2.0000 0.0000 0.0000 1.8038 7.3852 0.0000
-1.0000 0.0000 95.6300 6.2293 5.2294 0.1542 0.8563 0.0000
-3.2224 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
Au 1.8503 1.0000 196.9665 1.9219 0.1582 0.8218 -1.0000 1.0000
12.1238 4.0351 1.0000 0.0000 0.0000 1.8038 7.3852 0.0000
-1.0000 0.0000 72.6300 6.2293 5.2294 0.1542 0.8563 0.0000
-3.2224 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000
V 2.2657 3.0000 50.9415 1.7992 0.3005 0.6743 0.1000 5.0000
12.3879 5.2243 3.0000 0.0000 0.0000 -0.3628 6.6023 0.0000
-1.0000 0.0000 117.6300 23.1946 6.5795 0.0000 0.8563 0.0000
-3.5389 1.5012 1.0338 3.0000 3.6411 0.0000 0.0000 0.0000
Bi 2.1949 3.0000 208.9804 2.4429 0.1607 0.4960 0.0535 5.0000
12.9571 35.5167 3.0000 0.0000 0.0000 -0.1926 6.4153 0.0000
-1.0000 0.5785 52.6300 3.8978 0.9856 0.0314 0.8563 0.0000
-2.5000 5.0597 1.0338 6.0000 2.5791 0.0000 0.0000 0.0000
Ti 0.1000 4.0000 47.8800 2.0000 0.1659 0.6037 0.1000 4.0000
13.2535 4.0063 4.0000 -5.0000 0.0000 -0.1864 5.9304 0.0000
-1.0000 0.0000 129.6300 22.8461 1.8515 0.0064 0.8563 0.0000
-3.4122 3.2711 1.0338 6.2998 2.2632 0.0000 0.0000 0.0000
Mo 2.4710 5.6504 95.9400 1.8000 0.3285 1.0000 0.1000 6.0000
13.0000 45.0000 4.0000 0.0000 0.0000 0.6062 6.1484 0.0000
0.1000 0.0000 152.6300 3.7659 0.0689 2.9902 0.8563 0.0000
-16.7660 3.1072 1.0338 8.0000 3.4590 0.0000 0.0000 0.0000
X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000
10.0000 2.5000 4.0000 0.0000 0.0000 8.5000 1.5000 0.0000
-0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.9745 0.0000
-11.0000 2.7466 1.0338 2.0000 2.8793 0.0000 0.0000 0.0000
40 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6
pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr
1 1 158.2004 99.1897 78.0000 -0.7738 -0.4550 1.0000 37.6117 0.4147
0.4590 -0.1000 9.1628 1.0000 -0.0777 6.7268 1.0000 0.0000
1 2 169.4760 0.0000 0.0000 -0.6083 0.0000 1.0000 6.0000 0.7652
5.2290 1.0000 0.0000 1.0000 -0.0500 6.9136 0.0000 0.0000
2 2 166.8880 0.0000 0.0000 -0.2191 0.0000 1.0000 6.0000 1.0000
6.1152 1.0000 0.0000 1.0000 -0.0889 6.0000 0.0000 0.0000
1 3 158.6946 107.4583 23.3136 -0.4240 -0.1743 1.0000 10.8209 1.0000
0.5322 -0.3113 7.0000 1.0000 -0.1447 5.2450 0.0000 0.0000
3 3 200.0000 230.7321 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051
0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000
1 4 134.1215 140.2179 79.9745 0.0163 -0.1428 1.0000 27.0617 0.2000
0.1387 -0.3681 7.1611 1.0000 -0.1000 5.0825 1.0000 0.0000
3 4 130.8596 169.4551 40.0000 0.3837 -0.1639 1.0000 35.0000 0.2000
1.0000 -0.3579 7.0004 1.0000 -0.1193 6.8773 1.0000 0.0000
4 4 157.9384 82.5526 152.5336 0.4010 -0.1034 1.0000 12.4261 0.5828
0.1578 -0.1509 11.9186 1.0000 -0.0861 5.4271 1.0000 0.0000
2 3 163.1043 0.0000 0.0000 -0.4155 0.0000 1.0000 6.0000 0.3607
1.9380 1.0000 0.0000 0.0000 -0.0778 4.3082 0.0000 0.0000
2 4 231.8173 0.0000 0.0000 -0.3364 0.0000 1.0000 6.0000 0.4402
8.8910 1.0000 0.0000 1.0000 -0.0327 6.5754 0.0000 0.0000
1 5 128.9942 74.5848 55.2528 0.1035 -0.5211 1.0000 18.9617 0.6000
0.2949 -0.2398 8.1175 1.0000 -0.1029 5.6731 1.0000 0.0000
2 5 151.5159 0.0000 0.0000 -0.4721 0.0000 1.0000 6.0000 0.6000
9.4366 1.0000 0.0000 1.0000 -0.0290 7.0050 1.0000 0.0000
3 5 0.0000 0.0000 0.0000 0.5563 -0.4038 1.0000 49.5611 0.6000
0.4259 -0.4577 12.7569 1.0000 -0.1100 7.1145 1.0000 0.0000
4 5 0.0000 0.0000 0.0000 0.4438 -0.2034 1.0000 40.3399 0.6000
0.3296 -0.3153 9.1227 1.0000 -0.1805 5.6864 1.0000 0.0000
5 5 96.1871 93.7006 68.6860 0.0955 -0.4781 1.0000 17.8574 0.6000
0.2723 -0.2373 9.7875 1.0000 -0.0950 6.4757 1.0000 0.0000
6 6 109.1904 70.8314 30.0000 0.2765 -0.3000 1.0000 16.0000 0.1583
0.2804 -0.1994 8.1117 1.0000 -0.0675 8.2993 0.0000 0.0000
2 6 137.1002 0.0000 0.0000 -0.1902 0.0000 1.0000 6.0000 0.4256
17.7186 1.0000 0.0000 1.0000 -0.0377 6.4281 0.0000 0.0000
3 6 191.1743 52.0733 43.3991 -0.2584 -0.3000 1.0000 36.0000 0.8764
1.0248 -0.3658 4.2151 1.0000 -0.5004 4.2605 1.0000 0.0000
4 6 185.4488 39.2832 43.3991 -0.1922 -0.3000 1.0000 36.0000 0.8217
0.8538 -0.3887 4.4334 1.0000 -0.5241 4.4529 1.0000 0.0000
7 7 90.1462 0.0000 0.0000 0.0004 -0.2000 0.0000 16.0000 0.3484
1.0000 -0.2000 15.0000 1.0000 -0.1014 5.7631 0.0000 0.0000
8 8 85.2900 0.0000 0.0000 0.0004 -0.2000 0.0000 16.0000 0.5438
1.0000 -0.2000 15.0000 1.0000 -0.1001 5.5699 0.0000 0.0000
9 9 73.6182 0.0000 0.0000 0.0004 -0.2000 0.0000 16.0000 0.3418
1.0000 -0.2000 15.0000 1.0000 -0.1015 5.7850 0.0000 0.0000
10 10 73.6182 0.0000 0.0000 0.0004 -0.2000 0.0000 16.0000 0.3418
1.0000 -0.2000 15.0000 1.0000 -0.1015 5.7850 0.0000 0.0000
11 11 36.2751 0.0000 0.0000 0.8059 -0.3000 0.0000 16.0000 0.1826
0.3414 -0.3000 16.0000 1.0000 -0.0717 7.9108 0.0000 0.0000
3 11 106.8008 67.5543 0.0000 0.0323 -0.3000 1.0000 36.0000 0.1000
0.2670 -0.3402 16.0000 1.0000 -0.1761 4.6698 1.0000 0.0000
2 11 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
1 11 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
12 12 66.0677 0.0000 0.0000 -0.9557 -0.2000 0.0000 16.0000 0.2865
0.5847 -0.2000 15.0000 1.0000 -0.0856 5.2857 0.0000 0.0000
3 12 152.2407 57.6204 0.0000 -0.8033 -0.3000 1.0000 36.0000 0.0498
1.8097 -0.3800 16.0000 1.0000 -0.2379 8.0000 1.0000 0.0000
2 12 95.9209 0.0000 0.0000 -0.0153 -0.3000 1.0000 36.0000 0.0100
1.0000 -0.2062 8.6647 1.0000 -0.1911 4.0000 1.0000 0.0000
1 12 78.9091 40.6322 0.0000 0.0040 -0.3000 1.0000 36.0000 0.0384
0.0904 -0.1209 12.3682 1.0000 -0.1613 4.3849 1.0000 0.0000
13 13 71.3016 10.0000 0.0000 -0.1571 -0.2000 0.0000 16.0000 0.3311
0.1822 -0.2000 15.0000 1.0000 -0.1860 6.5172 0.0000 0.0000
3 13 112.7130 29.8084 0.0000 -0.9010 -0.3000 1.0000 36.0000 0.5508
0.1006 -0.2492 16.9476 1.0000 -0.1919 5.4797 1.0000 0.0000
1 13 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
2 13 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.2500 20.0000 1.0000 -0.2578 6.5219 1.0000 0.0000
1 14 0.5356 0.9614 0.0000 0.3817 -0.3000 1.0000 36.0000 0.2142
0.6116 -0.2579 6.1366 1.0000 -0.0913 6.6008 1.0000 0.0000
2 14 0.0000 0.0000 0.0000 -0.2872 -0.3000 1.0000 36.0000 0.0082
1.7973 -0.3027 4.6243 1.0000 -0.4578 3.5219 1.0000 0.0000
3 14 112.7070 10.0000 135.5011 0.9277 -0.2354 1.0000 19.1731 1.2334
0.9822 -0.1837 7.2216 1.0000 -0.1264 6.1257 1.0000 0.0000
14 14 44.6382 0.0000 0.0000 1.0000 -0.3000 0.0000 16.0000 0.2890
0.3384 -0.3000 16.0000 1.0000 -0.1862 7.4588 0.0000 0.0000
12 14 50.0000 0.0000 0.0000 0.1000 -0.3000 0.0000 16.0000 0.3000
1.0000 -0.3000 16.0000 1.0000 -0.2000 8.0000 0.0000 0.0000
20 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2
1 2 0.1239 1.4004 9.8467 1.1210 -1.0000 -1.0000
2 3 0.0299 1.3153 10.9102 0.9093 -1.0000 -1.0000
2 4 0.1059 1.8290 9.7818 0.9598 -1.0000 -1.0000
1 3 0.1156 1.8520 9.8317 1.2854 1.1352 1.0706
1 4 0.1447 1.8766 9.7990 1.3436 1.1885 1.1363
3 4 0.1048 2.0003 10.1220 1.3173 1.1096 1.0206
2 6 0.0470 1.6738 11.6877 1.1931 -1.0000 -1.0000
3 6 0.1263 1.8163 10.6833 1.6266 1.2052 -1.0000
1 11 0.1995 2.2133 13.0000 0.0102 1.4868 -1.0000
2 11 0.1319 1.5855 12.5457 0.0099 1.5065 -1.0000
3 11 0.0813 1.8649 10.8791 1.6498 1.6445 -1.0000
1 12 0.4235 1.7716 11.3664 1.8000 1.7212 -1.0000
2 12 0.0754 1.6033 12.4204 1.6896 -1.5000 -1.0000
3 12 0.1648 2.1260 11.2425 2.0692 1.6939 -1.0000
2 13 0.1340 1.8546 11.5784 1.0000 -1.0000 -1.0000
3 13 0.1280 1.8000 10.5743 1.7358 1.5296 -1.0000
1 13 0.1301 1.9382 11.1255 0.0100 -1.0000 -1.0000
1 14 0.1495 2.0794 12.2376 0.0100 1.4060 -1.0000
2 14 0.0795 1.6794 11.2376 0.0100 1.2060 -1.0000
3 14 0.2101 2.0342 10.4729 1.6019 1.4781 1.6548
97 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2
1 1 1 59.0573 30.7029 0.7606 0.0000 0.7180 6.2933 1.1244
1 1 2 65.7758 14.5234 6.2481 0.0000 0.5665 0.0000 1.6255
2 1 2 70.2607 25.2202 3.7312 0.0000 0.0050 0.0000 2.7500
1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400
1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400
2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400
1 1 3 49.6811 7.1713 4.3889 0.0000 0.7171 10.2661 1.0463
3 1 3 77.7473 40.1718 2.9802 -25.3063 1.6170 -46.1315 2.2503
1 1 4 66.1305 12.4661 7.0000 0.0000 3.0000 50.0000 1.1880
3 1 4 73.9544 12.4661 7.0000 0.0000 3.0000 0.0000 1.1880
4 1 4 64.1581 12.4661 7.0000 0.0000 3.0000 0.0000 1.1880
2 1 3 65.0000 13.8815 5.0583 0.0000 0.4985 0.0000 1.4900
2 1 4 74.2929 31.0883 2.6184 0.0000 0.0755 0.0000 1.0500
1 2 4 0.0000 0.0019 6.3000 0.0000 0.0000 0.0000 1.0400
1 3 1 73.5312 44.7275 0.7354 0.0000 3.0000 0.0000 1.0684
1 3 3 79.4761 36.3701 1.8943 0.0000 0.7351 67.6777 3.0000
1 3 4 82.4890 31.4554 0.9953 0.0000 1.6310 0.0000 1.0783
3 3 3 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783
3 3 4 84.3637 31.4554 0.9953 0.0000 1.6310 0.0000 1.0783
4 3 4 89.7071 31.4554 0.9953 0.0000 1.6310 0.0000 1.1519
1 3 2 70.1880 20.9562 0.3864 0.0000 0.0050 0.0000 1.6924
2 3 3 75.6935 25.0000 2.0000 0.0000 1.0000 0.0000 1.1680
2 3 4 75.6201 18.7919 0.9833 0.0000 0.1218 0.0000 1.0500
2 3 2 77.3619 4.8342 7.1628 0.0000 2.9933 0.0000 1.5948
1 4 1 66.0330 22.0295 1.4442 0.0000 1.6777 0.0000 1.0500
1 4 3 103.3204 33.0381 0.5787 0.0000 1.6777 0.0000 1.0500
1 4 4 104.1335 8.6043 1.6495 0.0000 1.6777 0.0000 1.0500
3 4 3 74.1978 42.1786 1.7845 -18.0069 1.6777 0.0000 1.0500
3 4 4 74.8600 43.7354 1.1572 -0.9193 1.6777 0.0000 1.0500
4 4 4 75.0538 14.8267 5.2794 0.0000 1.6777 0.0000 1.0500
1 4 2 69.1106 25.5067 1.1003 0.0000 0.0222 0.0000 1.0369
2 4 3 81.3686 40.0712 2.2396 0.0000 0.0222 0.0000 1.0369
2 4 4 83.0104 43.4766 1.5328 0.0000 0.0222 0.0000 1.0500
2 4 2 70.8687 12.0168 5.0132 0.0000 0.0222 0.0000 1.1243
1 2 3 0.0000 25.0000 3.0000 0.0000 1.0000 0.0000 1.0400
1 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
1 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
3 2 3 0.0000 4.4124 2.5758 0.0000 0.0000 0.0000 2.9884
3 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
4 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
2 2 3 0.0000 15.0000 2.2970 0.0000 0.0000 0.0000 1.3268
2 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
1 1 5 74.9397 25.0560 1.8787 0.1463 0.0559 0.0000 1.0400
1 5 1 86.9521 36.9951 2.0903 0.1463 0.0559 0.0000 1.0400
2 1 5 74.9397 25.0560 1.8787 0.0000 0.0000 0.0000 1.0400
1 5 2 86.1791 36.9951 2.0903 0.0000 0.0000 0.0000 1.0400
1 5 5 85.3644 36.9951 2.0903 0.1463 0.0559 0.0000 1.0400
2 5 2 93.1959 36.9951 2.0903 0.0000 0.0000 0.0000 1.0400
2 5 5 84.3331 36.9951 2.0903 0.0000 0.0000 0.0000 1.0400
6 6 6 69.3456 21.7361 1.4283 0.0000 -0.2101 0.0000 1.3241
2 6 6 75.6168 21.5317 1.0435 0.0000 2.5179 0.0000 1.0400
2 6 2 78.3939 20.9772 0.8630 0.0000 2.8421 0.0000 1.0400
3 6 6 70.3016 15.4081 1.3267 0.0000 2.1459 0.0000 1.0400
2 6 3 73.8232 16.6592 3.7425 0.0000 0.8613 0.0000 1.0400
3 6 3 90.0344 7.7656 1.7264 0.0000 0.7689 0.0000 1.0400
6 3 6 22.1715 3.6615 0.3160 0.0000 4.1125 0.0000 1.0400
2 3 6 83.7634 5.6693 2.7780 0.0000 1.6982 0.0000 1.0400
3 3 6 73.4663 25.0761 0.9143 0.0000 2.2466 0.0000 1.0400
2 2 6 0.0000 47.1300 6.0000 0.0000 1.6371 0.0000 1.0400
6 2 6 0.0000 31.5209 6.0000 0.0000 1.6371 0.0000 1.0400
3 2 6 0.0000 31.0427 4.5625 0.0000 1.6371 0.0000 1.0400
2 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
3 11 3 62.4906 31.5023 1.3328 0.0000 2.8731 0.0000 1.0794
11 3 11 31.0790 19.3435 0.4919 0.0000 2.9625 0.0000 3.0000
3 3 11 100.0000 14.7642 7.0000 0.0000 1.0585 0.0000 1.1599
1 3 11 60.7895 13.6681 0.7546 0.0000 2.1747 0.0000 2.9508
2 3 11 100.0000 5.0000 1.4335 0.0000 1.2363 0.0000 5.0000
3 12 12 23.8296 8.9089 7.0000 0.0000 1.0000 0.0000 2.8891
3 12 3 87.0764 19.4489 2.5080 0.0000 2.6056 0.0000 3.0000
12 3 12 72.7369 13.7522 5.0243 0.0000 2.9700 0.0000 1.5506
3 3 12 68.8771 10.5000 2.5500 0.0000 2.5729 0.0000 1.5892
2 3 12 99.5836 5.4142 2.2105 0.0000 1.0513 0.0000 1.1000
1 3 12 90.0000 12.1772 2.2055 0.0000 1.9064 0.0000 2.6056
1 1 12 71.1708 32.6379 0.4516 0.0000 2.1609 0.0000 1.1000
1 12 3 90.0000 45.0000 0.9335 0.0000 0.2140 0.0000 1.4846
1 12 1 87.6204 45.0000 1.2740 0.0000 1.1519 0.0000 1.1000
3 1 12 54.7020 3.2967 7.0000 0.0000 2.0408 0.0000 2.4032
2 12 3 90.0000 28.2099 1.8036 0.0000 1.5461 0.0000 1.2304
2 12 2 90.0000 36.3001 0.6409 0.0000 3.0000 0.0000 1.7755
1 12 2 89.5835 45.0000 0.8465 0.0000 1.2118 0.0000 2.2282
2 1 12 68.7714 22.9669 0.4631 0.0000 2.4269 0.0000 1.4680
2 2 12 0.0000 30.2898 3.9181 0.0000 0.9914 0.0000 1.3121
3 2 12 0.0000 1.0000 4.1706 0.0000 1.0100 0.0000 1.1000
1 2 12 0.0000 1.0000 3.9722 0.0000 1.0075 0.0000 1.2984
3 13 3 73.6321 10.6453 2.7693 0.0000 0.0500 0.0000 1.9906
13 3 13 100.0000 5.0270 5.0000 0.0000 1.2768 0.0000 2.0630
3 3 13 52.3127 40.0000 1.1362 0.0000 1.5100 0.0000 1.1000
3 13 13 66.6695 0.0036 3.2646 0.0000 0.0581 0.0000 1.3741
2 3 13 100.0000 3.8927 8.0000 0.0000 2.0000 0.0000 1.1000
1 3 13 96.6040 9.4537 8.0000 0.0000 0.3285 0.0000 4.0000
3 14 3 79.6765 50.0000 1.0502 -0.0016 0.1000 0.0000 1.4583
14 3 14 20.2100 37.6165 0.6059 0.0000 0.1531 0.0000 2.0586
3 3 14 38.5570 11.9307 0.9911 0.0000 0.8422 0.0000 1.0500
3 14 14 5.8342 0.0724 0.1000 0.0000 0.5490 0.0000 1.7839
2 3 14 81.8943 7.2820 2.1490 0.0000 0.6873 0.0000 3.2184
1 3 14 75.5634 8.3289 1.0236 0.0000 2.0875 0.0000 1.0500
12 3 14 30.0000 5.0000 0.5000 0.0000 0.5000 0.0000 1.2500
47 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n
1 1 1 1 -0.2500 34.7453 0.0288 -6.3507 -1.6000 0.0000 0.0000
1 1 1 2 -0.2500 29.2131 0.2945 -4.9581 -2.1802 0.0000 0.0000
2 1 1 2 -0.2500 31.2081 0.4539 -4.8923 -2.2677 0.0000 0.0000
1 1 1 3 -0.3495 22.2142 -0.2959 -2.5000 -1.9066 0.0000 0.0000
2 1 1 3 0.0646 24.3195 0.6259 -3.9603 -1.0000 0.0000 0.0000
3 1 1 3 -0.5456 5.5756 0.8433 -5.1924 -1.0180 0.0000 0.0000
1 1 3 1 1.7555 27.9267 0.0072 -2.6533 -1.0000 0.0000 0.0000
1 1 3 2 -1.4358 36.7830 -1.0000 -8.1821 -1.0000 0.0000 0.0000
2 1 3 1 -1.3959 34.5053 0.7200 -2.5714 -2.1641 0.0000 0.0000
2 1 3 2 -2.5000 70.0597 1.0000 -3.5539 -2.9929 0.0000 0.0000
1 1 3 3 0.6852 11.2819 -0.4784 -2.5000 -2.1085 0.0000 0.0000
2 1 3 3 0.1933 80.0000 1.0000 -4.0590 -3.0000 0.0000 0.0000
3 1 3 1 -1.9889 76.4820 -0.1796 -3.8301 -3.0000 0.0000 0.0000
3 1 3 2 0.2160 72.7707 -0.7087 -4.2100 -3.0000 0.0000 0.0000
3 1 3 3 -2.5000 71.0772 0.2542 -3.1631 -3.0000 0.0000 0.0000
1 3 3 1 2.5000 -0.6002 1.0000 -3.4297 -2.8858 0.0000 0.0000
1 3 3 2 -2.5000 -3.3822 0.7004 -5.4467 -2.9586 0.0000 0.0000
2 3 3 2 2.5000 -4.0000 0.9000 -2.5000 -1.0000 0.0000 0.0000
1 3 3 3 1.2329 -4.0000 1.0000 -2.5000 -1.7479 0.0000 0.0000
2 3 3 3 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 0.0000 0.0000
3 3 3 3 -2.5000 -4.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000
0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000
0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000
0 1 4 0 -2.4242 128.1636 0.3739 -6.6098 -2.0000 0.0000 0.0000
0 2 4 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
0 3 4 0 1.4816 55.6641 0.0004 -7.0465 -2.7203 0.0000 0.0000
0 4 4 0 -0.3244 27.7086 0.0039 -2.8272 -2.0000 0.0000 0.0000
4 1 4 4 -5.5181 8.9706 0.0004 -6.1782 -2.0000 0.0000 0.0000
0 1 5 0 3.3423 30.3435 0.0365 -2.7171 0.0000 0.0000 0.0000
0 5 5 0 -0.0555 -42.7738 0.1515 -2.2056 0.0000 0.0000 0.0000
0 2 5 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 6 6 0 0.0000 0.0000 0.1200 -2.4426 0.0000 0.0000 0.0000
0 2 6 0 0.0000 0.0000 0.1200 -2.4847 0.0000 0.0000 0.0000
0 3 6 0 0.0000 0.0000 0.1200 -2.4703 0.0000 0.0000 0.0000
2 1 3 14 1.6297 56.8132 0.3398 -2.6912 -2.1000 0.0000 0.0000
1 1 3 14 -0.0427 13.4096 0.9351 -6.5245 -2.1000 0.0000 0.0000
2 3 14 3 2.5000 11.6208 1.0000 -9.0000 -1.0000 0.0000 0.0000
2 1 3 12 -0.2500 45.7639 0.3000 -3.5745 -2.1565 0.0000 0.0000
1 1 3 12 -0.2500 69.1094 0.3000 -3.0983 -2.1565 0.0000 0.0000
2 3 12 3 -0.4306 7.5000 -0.5000 -6.9948 -1.0000 0.0000 0.0000
2 3 11 3 1.8627 9.7180 -1.0000 -7.2224 -1.0000 0.0000 0.0000
1 3 11 3 2.5000 23.9443 1.0000 -3.2267 -1.0000 0.0000 0.0000
1 1 3 11 0.9114 62.5039 -0.2389 -3.2976 -1.0000 0.0000 0.0000
2 1 3 11 0.5000 35.0000 0.5000 -4.0000 -1.0000 0.0000 0.0000
9 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1
3 2 3 2.1845 -2.3549 3.0582 19.1627
3 2 4 2.0000 -6.0000 1.7976 3.0000
4 2 3 1.2000 -2.0000 1.7976 3.0000
4 2 4 1.2979 -6.0000 1.7976 3.0000
3 2 5 1.5000 -2.0000 1.7976 3.0000
4 2 5 1.5000 -2.0000 1.7976 3.0000
5 2 3 1.5000 -2.0000 1.7976 3.0000
5 2 4 1.5000 -2.0000 1.7976 3.0000
5 2 5 1.5000 -2.0000 1.7976 3.0000
environ/param.gpu.water
+ 3
− 0
View file @ 70d872fe
......@@ -59,3 +59,6 @@ freq_dipole_anal 1 ! calculate electric dipole mome
diffusion_coef 0 ! 1: calculate diffusion coefficient of the system
freq_diffusion_coef 1 ! calculate diffusion coefficient at every 'this many' steps
restrict_type 2 ! -1: all types of atoms, 0 and up: only this type of atoms
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
restart_freq 0 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
sPuReMD/src/charges.c
+ 385
− 322
View file @ 70d872fe
......@@ -1420,7 +1420,7 @@ static void Extrapolate_Charges_QEq( const reax_system * const system,
}
static void Extrapolate_Charges_EEM( const reax_system * const system,
static void Extrapolate_Charges_EE( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace )
{
......@@ -1430,7 +1430,7 @@ static void Extrapolate_Charges_EEM( const reax_system * const system,
/* extrapolation for s */
//TODO: good candidate for vectorization, avoid moving data with head pointer and circular buffer
#pragma omp parallel for schedule(static) \
default(none) private(i, s_tmp)
default(none) private(i, s_tmp)
for ( i = 0; i < system->N_cm; ++i )
{
// no extrapolation
......@@ -1466,6 +1466,7 @@ static void Compute_Preconditioner_QEq( const reax_system * const system,
simulation_data * const data, static_storage * const workspace,
const list * const far_nbrs )
{
real time;
sparse_matrix *Hptr;
if ( control->cm_domain_sparsify_enabled == TRUE )
......@@ -1477,6 +1478,22 @@ static void Compute_Preconditioner_QEq( const reax_system * const system,
Hptr = workspace->H;
}
time = Get_Time( );
if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
{
if ( control->cm_domain_sparsify_enabled == TRUE )
{
Hptr = setup_graph_coloring( workspace->H_sp );
}
else
{
Hptr = setup_graph_coloring( workspace->H );
}
Sort_Matrix_Rows( Hptr );
}
data->timing.cm_sort_mat_rows += Get_Timing_Info( time );
#if defined(TEST_MAT)
Hptr = create_test_mat( );
#endif
......@@ -1527,53 +1544,300 @@ static void Compute_Preconditioner_QEq( const reax_system * const system,
#if defined(DEBUG_FOCUS)
sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
Print_Sparse_Matrix2( workspace->L, fname );
Print_Sparse_Matrix2( workspace->L, fname, NULL );
sprintf( fname, "%s.U%d.out", control->sim_name, data->step );
Print_Sparse_Matrix2( workspace->U, fname );
fprintf( stderr, "icholt-" );
//sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
//Print_Sparse_Matrix2( workspace->L, fname );
//Print_Sparse_Matrix( U );
Print_Sparse_Matrix2( workspace->U, fname, NULL );
#endif
}
#endif
}
/* Compute preconditioner for EEM
/* Compute preconditioner for EE
*/
static void Compute_Preconditioner_EEM( const reax_system * const system,
//static void Compute_Preconditioner_EE( const reax_system * const system,
// const control_params * const control,
// simulation_data * const data, static_storage * const workspace,
// const list * const far_nbrs )
//{
// int i, top;
// static real * ones = NULL, * x = NULL, * y = NULL;
// sparse_matrix *Hptr;
//
// Hptr = workspace->H_EE;
//
//#if defined(TEST_MAT)
// Hptr = create_test_mat( );
//#endif
//
// if ( ones == NULL )
// {
// if ( ( ones = (real*) malloc( system->N * sizeof(real)) ) == NULL ||
// ( x = (real*) malloc( system->N * sizeof(real)) ) == NULL ||
// ( y = (real*) malloc( system->N * sizeof(real)) ) == NULL )
// {
// fprintf( stderr, "Not enough space for preconditioner computation. Terminating...\n" );
// exit( INSUFFICIENT_MEMORY );
// }
//
// for ( i = 0; i < system->N; ++i )
// {
// ones[i] = 1.0;
// }
// }
//
// switch ( control->cm_solver_pre_comp_type )
// {
// case DIAG_PC:
// data->timing.cm_solver_pre_comp +=
// diag_pre_comp( Hptr, workspace->Hdia_inv );
// break;
//
// case ICHOLT_PC:
// data->timing.cm_solver_pre_comp +=
// ICHOLT( Hptr, workspace->droptol, workspace->L_EE, workspace->U_EE );
// break;
//
// case ILU_PAR_PC:
// data->timing.cm_solver_pre_comp +=
// ILU_PAR( Hptr, control->cm_solver_pre_comp_sweeps, workspace->L_EE, workspace->U_EE );
// break;
//
// case ILUT_PAR_PC:
// data->timing.cm_solver_pre_comp +=
// ILUT_PAR( Hptr, workspace->droptol, control->cm_solver_pre_comp_sweeps,
// workspace->L_EE, workspace->U_EE );
// break;
//
// case ILU_SUPERLU_MT_PC:
//#if defined(HAVE_SUPERLU_MT)
// data->timing.cm_solver_pre_comp +=
// SuperLU_Factorize( Hptr, workspace->L_EE, workspace->U_EE );
//#else
// fprintf( stderr, "SuperLU MT support disabled. Re-compile before enabling. Terminating...\n" );
// exit( INVALID_INPUT );
//#endif
// break;
//
// default:
// fprintf( stderr, "Unrecognized preconditioner computation method. Terminating...\n" );
// exit( INVALID_INPUT );
// break;
// }
//
// if ( control->cm_solver_pre_comp_type != DIAG_PC )
// {
// switch ( control->cm_solver_pre_app_type )
// {
// case TRI_SOLVE_PA:
// tri_solve( workspace->L_EE, ones, x, workspace->L_EE->n, LOWER );
// Transpose_I( workspace->U_EE );
// tri_solve( workspace->U_EE, ones, y, workspace->U_EE->n, LOWER );
// Transpose_I( workspace->U_EE );
//
// memcpy( workspace->L->start, workspace->L_EE->start, sizeof(unsigned int) * (system->N + 1) );
// memcpy( workspace->L->j, workspace->L_EE->j, sizeof(unsigned int) * workspace->L_EE->start[workspace->L_EE->n] );
// memcpy( workspace->L->val, workspace->L_EE->val, sizeof(real) * workspace->L_EE->start[workspace->L_EE->n] );
//
// top = workspace->L->start[system->N];
// for ( i = 0; i < system->N; ++i )
// {
// workspace->L->j[top] = i;
// workspace->L->val[top] = x[i];
// ++top;
// }
//
// workspace->L->j[top] = system->N_cm - 1;
// workspace->L->val[top] = 1.0;
// ++top;
//
// workspace->L->start[system->N_cm] = top;
//
// top = 0;
// for ( i = 0; i < system->N; ++i )
// {
// workspace->U->start[i] = top;
// memcpy( workspace->U->j + top, workspace->U_EE->j + workspace->U_EE->start[i],
// sizeof(unsigned int) * (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]) );
// memcpy( workspace->U->val + top, workspace->U_EE->val + workspace->U_EE->start[i],
// sizeof(real) * (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]) );
// top += (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]);
//
// workspace->U->j[top] = system->N_cm - 1;
// workspace->U->val[top] = y[i];
// ++top;
// }
//
// workspace->U->start[system->N_cm - 1] = top;
//
// workspace->U->j[top] = system->N_cm - 1;
// workspace->U->val[top] = -Dot( x, y, system->N );
// ++top;
//
// workspace->U->start[system->N_cm] = top;
// break;
//
// case TRI_SOLVE_LEVEL_SCHED_PA:
// tri_solve_level_sched( workspace->L_EE, ones, x, workspace->L_EE->n, LOWER, TRUE );
// Transpose_I( workspace->U_EE );
// tri_solve_level_sched( workspace->U_EE, ones, y, workspace->U_EE->n, LOWER, TRUE );
// Transpose_I( workspace->U_EE );
//
// memcpy( workspace->L->start, workspace->L_EE->start, sizeof(unsigned int) * (system->N + 1) );
// memcpy( workspace->L->j, workspace->L_EE->j, sizeof(unsigned int) * workspace->L_EE->start[workspace->L_EE->n] );
// memcpy( workspace->L->val, workspace->L_EE->val, sizeof(real) * workspace->L_EE->start[workspace->L_EE->n] );
//
// top = workspace->L->start[system->N];
// for ( i = 0; i < system->N; ++i )
// {
// workspace->L->j[top] = i;
// workspace->L->val[top] = x[i];
// ++top;
// }
//
// workspace->L->j[top] = system->N_cm - 1;
// workspace->L->val[top] = 1.0;
// ++top;
//
// workspace->L->start[system->N_cm] = top;
//
// top = 0;
// for ( i = 0; i < system->N; ++i )
// {
// workspace->U->start[i] = top;
// memcpy( workspace->U->j + top, workspace->U_EE->j + workspace->U_EE->start[i],
// sizeof(unsigned int) * (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]) );
// memcpy( workspace->U->val + top, workspace->U_EE->val + workspace->U_EE->start[i],
// sizeof(real) * (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]) );
// top += (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]);
//
// workspace->U->j[top] = system->N_cm - 1;
// workspace->U->val[top] = y[i];
// ++top;
// }
//
// workspace->U->start[system->N_cm - 1] = top;
//
// workspace->U->j[top] = system->N_cm - 1;
// workspace->U->val[top] = -Dot( x, y, system->N );
// ++top;
//
// workspace->U->start[system->N_cm] = top;
// break;
//
// //TODO: add Jacobi iter, etc.?
// default:
// tri_solve( workspace->L_EE, ones, x, workspace->L_EE->n, LOWER );
// Transpose_I( workspace->U_EE );
// tri_solve( workspace->U_EE, ones, y, workspace->U_EE->n, LOWER );
// Transpose_I( workspace->U_EE );
//
// memcpy( workspace->L->start, workspace->L_EE->start, sizeof(unsigned int) * (system->N + 1) );
// memcpy( workspace->L->j, workspace->L_EE->j, sizeof(unsigned int) * workspace->L_EE->start[workspace->L_EE->n] );
// memcpy( workspace->L->val, workspace->L_EE->val, sizeof(real) * workspace->L_EE->start[workspace->L_EE->n] );
//
// top = workspace->L->start[system->N];
// for ( i = 0; i < system->N; ++i )
// {
// workspace->L->j[top] = i;
// workspace->L->val[top] = x[i];
// ++top;
// }
//
// workspace->L->j[top] = system->N_cm - 1;
// workspace->L->val[top] = 1.0;
// ++top;
//
// workspace->L->start[system->N_cm] = top;
//
// top = 0;
// for ( i = 0; i < system->N; ++i )
// {
// workspace->U->start[i] = top;
// memcpy( workspace->U->j + top, workspace->U_EE->j + workspace->U_EE->start[i],
// sizeof(unsigned int) * (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]) );
// memcpy( workspace->U->val + top, workspace->U_EE->val + workspace->U_EE->start[i],
// sizeof(real) * (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]) );
// top += (workspace->U_EE->start[i + 1] - workspace->U_EE->start[i]);
//
// workspace->U->j[top] = system->N_cm - 1;
// workspace->U->val[top] = y[i];
// ++top;
// }
//
// workspace->U->start[system->N_cm - 1] = top;
//
// workspace->U->j[top] = system->N_cm - 1;
// workspace->U->val[top] = -Dot( x, y, system->N );
// ++top;
//
// workspace->U->start[system->N_cm] = top;
// break;
// }
// }
//
//#if defined(DEBUG)
// if ( control->cm_solver_pre_comp_type != DIAG_PC )
// {
// fprintf( stderr, "condest = %f\n", condest(workspace->L) );
//
//#if defined(DEBUG_FOCUS)
// sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
// Print_Sparse_Matrix2( workspace->L, fname, NULL );
// sprintf( fname, "%s.U%d.out", control->sim_name, data->step );
// Print_Sparse_Matrix2( workspace->U, fname, NULL );
//
// fprintf( stderr, "icholt-" );
// sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
// Print_Sparse_Matrix2( workspace->L, fname, NULL );
// Print_Sparse_Matrix( U );
//#endif
// }
//#endif
//}
/* Compute preconditioner for EE
*/
static void Compute_Preconditioner_EE( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace,
const list * const far_nbrs )
{
int i, top;
static real * ones = NULL, * x = NULL, * y = NULL;
real time;
sparse_matrix *Hptr;
Hptr = workspace->H_EEM;
#if defined(TEST_MAT)
Hptr = create_test_mat( );
#endif
if ( control->cm_domain_sparsify_enabled == TRUE )
{
Hptr = workspace->H_sp;
}
else
{
Hptr = workspace->H;
}
if ( ones == NULL )
time = Get_Time( );
if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
{
if ( ( ones = (real*) malloc( system->N * sizeof(real)) ) == NULL ||
( x = (real*) malloc( system->N * sizeof(real)) ) == NULL ||
( y = (real*) malloc( system->N * sizeof(real)) ) == NULL )
if ( control->cm_domain_sparsify_enabled == TRUE )
{
fprintf( stderr, "Not enough space for preconditioner computation. Terminating...\n" );
exit( INSUFFICIENT_MEMORY );
Hptr = setup_graph_coloring( workspace->H_sp );
}
for ( i = 0; i < system->N; ++i )
else
{
ones[i] = 1.0;
Hptr = setup_graph_coloring( workspace->H );
}
Sort_Matrix_Rows( Hptr );
}
data->timing.cm_sort_mat_rows += Get_Timing_Info( time );
#if defined(TEST_MAT)
Hptr = create_test_mat( );
#endif
Hptr->val[Hptr->start[system->N + 1] - 1] = 1.0;
switch ( control->cm_solver_pre_comp_type )
{
case DIAG_PC:
......@@ -1583,24 +1847,24 @@ static void Compute_Preconditioner_EEM( const reax_system * const system,
case ICHOLT_PC:
data->timing.cm_solver_pre_comp +=
ICHOLT( Hptr, workspace->droptol, workspace->L_EEM, workspace->U_EEM );
ICHOLT( Hptr, workspace->droptol, workspace->L, workspace->U );
break;
case ILU_PAR_PC:
data->timing.cm_solver_pre_comp +=
ILU_PAR( Hptr, control->cm_solver_pre_comp_sweeps, workspace->L_EEM, workspace->U_EEM );
ILU_PAR( Hptr, control->cm_solver_pre_comp_sweeps, workspace->L, workspace->U );
break;
case ILUT_PAR_PC:
data->timing.cm_solver_pre_comp +=
ILUT_PAR( Hptr, workspace->droptol, control->cm_solver_pre_comp_sweeps,
workspace->L_EEM, workspace->U_EEM );
workspace->L, workspace->U );
break;
case ILU_SUPERLU_MT_PC:
#if defined(HAVE_SUPERLU_MT)
data->timing.cm_solver_pre_comp +=
SuperLU_Factorize( Hptr, workspace->L_EEM, workspace->U_EEM );
SuperLU_Factorize( Hptr, workspace->L, workspace->U );
#else
fprintf( stderr, "SuperLU MT support disabled. Re-compile before enabling. Terminating...\n" );
exit( INVALID_INPUT );
......@@ -1613,172 +1877,18 @@ static void Compute_Preconditioner_EEM( const reax_system * const system,
break;
}
if ( control->cm_solver_pre_comp_type != DIAG_PC )
{
switch ( control->cm_solver_pre_app_type )
{
case TRI_SOLVE_PA:
tri_solve( workspace->L_EEM, ones, x, workspace->L_EEM->n, LOWER );
Transpose_I( workspace->U_EEM );
tri_solve( workspace->U_EEM, ones, y, workspace->U_EEM->n, LOWER );
Transpose_I( workspace->U_EEM );
memcpy( workspace->L->start, workspace->L_EEM->start, sizeof(unsigned int) * (system->N + 1) );
memcpy( workspace->L->j, workspace->L_EEM->j, sizeof(unsigned int) * workspace->L_EEM->start[workspace->L_EEM->n] );
memcpy( workspace->L->val, workspace->L_EEM->val, sizeof(real) * workspace->L_EEM->start[workspace->L_EEM->n] );
top = workspace->L->start[system->N];
for ( i = 0; i < system->N; ++i )
{
workspace->L->j[top] = i;
workspace->L->val[top] = x[i];
++top;
}
workspace->L->j[top] = system->N_cm - 1;
workspace->L->val[top] = 1.0;
++top;
workspace->L->start[system->N_cm] = top;
top = 0;
for ( i = 0; i < system->N; ++i )
{
workspace->U->start[i] = top;
memcpy( workspace->U->j + top, workspace->U_EEM->j + workspace->U_EEM->start[i],
sizeof(unsigned int) * (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]) );
memcpy( workspace->U->val + top, workspace->U_EEM->val + workspace->U_EEM->start[i],
sizeof(real) * (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]) );
top += (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]);
workspace->U->j[top] = system->N_cm - 1;
workspace->U->val[top] = y[i];
++top;
}
workspace->U->start[system->N_cm - 1] = top;
workspace->U->j[top] = system->N_cm - 1;
workspace->U->val[top] = -Dot( x, y, system->N );
++top;
workspace->U->start[system->N_cm] = top;
break;
case TRI_SOLVE_LEVEL_SCHED_PA:
tri_solve_level_sched( workspace->L_EEM, ones, x, workspace->L_EEM->n, LOWER, TRUE );
Transpose_I( workspace->U_EEM );
tri_solve_level_sched( workspace->U_EEM, ones, y, workspace->U_EEM->n, LOWER, TRUE );
Transpose_I( workspace->U_EEM );
memcpy( workspace->L->start, workspace->L_EEM->start, sizeof(unsigned int) * (system->N + 1) );
memcpy( workspace->L->j, workspace->L_EEM->j, sizeof(unsigned int) * workspace->L_EEM->start[workspace->L_EEM->n] );
memcpy( workspace->L->val, workspace->L_EEM->val, sizeof(real) * workspace->L_EEM->start[workspace->L_EEM->n] );
top = workspace->L->start[system->N];
for ( i = 0; i < system->N; ++i )
{
workspace->L->j[top] = i;
workspace->L->val[top] = x[i];
++top;
}
workspace->L->j[top] = system->N_cm - 1;
workspace->L->val[top] = 1.0;
++top;
workspace->L->start[system->N_cm] = top;
top = 0;
for ( i = 0; i < system->N; ++i )
{
workspace->U->start[i] = top;
memcpy( workspace->U->j + top, workspace->U_EEM->j + workspace->U_EEM->start[i],
sizeof(unsigned int) * (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]) );
memcpy( workspace->U->val + top, workspace->U_EEM->val + workspace->U_EEM->start[i],
sizeof(real) * (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]) );
top += (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]);
workspace->U->j[top] = system->N_cm - 1;
workspace->U->val[top] = y[i];
++top;
}
workspace->U->start[system->N_cm - 1] = top;
workspace->U->j[top] = system->N_cm - 1;
workspace->U->val[top] = -Dot( x, y, system->N );
++top;
workspace->U->start[system->N_cm] = top;
break;
//TODO: add Jacobi iter, etc.?
default:
tri_solve( workspace->L_EEM, ones, x, workspace->L_EEM->n, LOWER );
Transpose_I( workspace->U_EEM );
tri_solve( workspace->U_EEM, ones, y, workspace->U_EEM->n, LOWER );
Transpose_I( workspace->U_EEM );
memcpy( workspace->L->start, workspace->L_EEM->start, sizeof(unsigned int) * (system->N + 1) );
memcpy( workspace->L->j, workspace->L_EEM->j, sizeof(unsigned int) * workspace->L_EEM->start[workspace->L_EEM->n] );
memcpy( workspace->L->val, workspace->L_EEM->val, sizeof(real) * workspace->L_EEM->start[workspace->L_EEM->n] );
top = workspace->L->start[system->N];
for ( i = 0; i < system->N; ++i )
{
workspace->L->j[top] = i;
workspace->L->val[top] = x[i];
++top;
}
workspace->L->j[top] = system->N_cm - 1;
workspace->L->val[top] = 1.0;
++top;
workspace->L->start[system->N_cm] = top;
top = 0;
for ( i = 0; i < system->N; ++i )
{
workspace->U->start[i] = top;
memcpy( workspace->U->j + top, workspace->U_EEM->j + workspace->U_EEM->start[i],
sizeof(unsigned int) * (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]) );
memcpy( workspace->U->val + top, workspace->U_EEM->val + workspace->U_EEM->start[i],
sizeof(real) * (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]) );
top += (workspace->U_EEM->start[i + 1] - workspace->U_EEM->start[i]);
workspace->U->j[top] = system->N_cm - 1;
workspace->U->val[top] = y[i];
++top;
}
workspace->U->start[system->N_cm - 1] = top;
workspace->U->j[top] = system->N_cm - 1;
workspace->U->val[top] = -Dot( x, y, system->N );
++top;
workspace->U->start[system->N_cm] = top;
break;
}
}
Hptr->val[Hptr->start[system->N + 1] - 1] = 0.0;
#if defined(DEBUG)
if ( control->cm_solver_pre_comp_type != DIAG_PC )
{
fprintf( stderr, "condest = %f\n", condest(workspace->L) );
fprintf( stderr, "condest = %f\n", condest(workspace->L, workspace->U) );
#if defined(DEBUG_FOCUS)
sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
Print_Sparse_Matrix2( workspace->L, fname );
Print_Sparse_Matrix2( workspace->L, fname, NULL );
sprintf( fname, "%s.U%d.out", control->sim_name, data->step );
Print_Sparse_Matrix2( workspace->U, fname );
fprintf( stderr, "icholt-" );
//sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
//Print_Sparse_Matrix2( workspace->L, fname );
//Print_Sparse_Matrix( U );
Print_Sparse_Matrix2( workspace->U, fname, NULL );
#endif
}
#endif
......@@ -1792,6 +1902,7 @@ static void Compute_Preconditioner_ACKS2( const reax_system * const system,
simulation_data * const data, static_storage * const workspace,
const list * const far_nbrs )
{
real time;
sparse_matrix *Hptr;
if ( control->cm_domain_sparsify_enabled == TRUE )
......@@ -1803,17 +1914,28 @@ static void Compute_Preconditioner_ACKS2( const reax_system * const system,
Hptr = workspace->H;
}
time = Get_Time( );
if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
{
if ( control->cm_domain_sparsify_enabled == TRUE )
{
Hptr = setup_graph_coloring( workspace->H_sp );
}
else
{
Hptr = setup_graph_coloring( workspace->H );
}
Sort_Matrix_Rows( Hptr );
}
data->timing.cm_sort_mat_rows += Get_Timing_Info( time );
#if defined(TEST_MAT)
Hptr = create_test_mat( );
#endif
// fprintf( stderr, "(%4d, %4d): %f\n", system->N, Hptr->j[Hptr->start[system->N + 1] - 1], Hptr->val[Hptr->start[system->N + 1] - 1] );
// fprintf( stderr, "(%4d, %4d): %f\n", system->N_cm - 1, Hptr->j[Hptr->start[system->N_cm] - 1], Hptr->val[Hptr->start[system->N_cm] - 1] );
Hptr->val[Hptr->start[system->N + 1] - 1] = 1.0;
Hptr->val[Hptr->start[system->N_cm] - 1] = 1.0;
// fprintf( stderr, "(%4d, %4d): %f\n", system->N, Hptr->j[Hptr->start[system->N + 1] - 1], Hptr->val[Hptr->start[system->N + 1] - 1] );
// fprintf( stderr, "(%4d, %4d): %f\n", system->N_cm - 1, Hptr->j[Hptr->start[system->N_cm] - 1], Hptr->val[Hptr->start[system->N_cm] - 1] );
// fflush( stderr );
switch ( control->cm_solver_pre_comp_type )
{
......@@ -1864,14 +1986,9 @@ static void Compute_Preconditioner_ACKS2( const reax_system * const system,
#if defined(DEBUG_FOCUS)
sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
Print_Sparse_Matrix2( workspace->L, fname );
Print_Sparse_Matrix2( workspace->L, fname, NULL );
sprintf( fname, "%s.U%d.out", control->sim_name, data->step );
Print_Sparse_Matrix2( workspace->U, fname );
fprintf( stderr, "icholt-" );
//sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
//Print_Sparse_Matrix2( workspace->L, fname );
//Print_Sparse_Matrix( U );
Print_Sparse_Matrix2( workspace->U, fname, NULL );
#endif
}
#endif
......@@ -1905,20 +2022,6 @@ static void Setup_Preconditioner_QEq( const reax_system * const system,
{
Sort_Matrix_Rows( workspace->H_sp );
}
if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
{
if ( control->cm_domain_sparsify_enabled == TRUE )
{
Hptr = setup_graph_coloring( workspace->H_sp );
}
else
{
Hptr = setup_graph_coloring( workspace->H );
}
Sort_Matrix_Rows( Hptr );
}
data->timing.cm_sort_mat_rows += Get_Timing_Info( time );
#if defined(DEBUG)
......@@ -2034,9 +2137,9 @@ static void Setup_Preconditioner_QEq( const reax_system * const system,
}
/* Setup routines before computing the preconditioner for EEM
/* Setup routines before computing the preconditioner for EE
*/
static void Setup_Preconditioner_EEM( const reax_system * const system,
static void Setup_Preconditioner_EE( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace,
const list * const far_nbrs )
......@@ -2061,45 +2164,14 @@ static void Setup_Preconditioner_EEM( const reax_system * const system,
{
Sort_Matrix_Rows( workspace->H_sp );
}
if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
{
if ( control->cm_domain_sparsify_enabled == TRUE )
{
Hptr = setup_graph_coloring( workspace->H_sp );
}
else
{
Hptr = setup_graph_coloring( workspace->H );
}
Sort_Matrix_Rows( Hptr );
}
data->timing.cm_sort_mat_rows += Get_Timing_Info( time );
Hptr->val[Hptr->start[system->N + 1] - 1] = 1.0;
#if defined(DEBUG)
fprintf( stderr, "H matrix sorted\n" );
#endif
if ( workspace->H_EEM == NULL )
{
if ( Allocate_Matrix( &(workspace->H_EEM), system->N, workspace->H->m ) == FAILURE )
{
fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
exit( INSUFFICIENT_MEMORY );
}
}
else
{
//TODO: reallocate
}
memcpy( workspace->H_EEM->start, Hptr->start, sizeof(unsigned int) * (system->N + 1) );
memcpy( workspace->H_EEM->j, Hptr->j, sizeof(unsigned int) * Hptr->start[system->N] );
memcpy( workspace->H_EEM->val, Hptr->val, sizeof(real) * Hptr->start[system->N] );
Hptr = workspace->H_EEM;
switch ( control->cm_solver_pre_comp_type )
{
case DIAG_PC:
......@@ -2130,9 +2202,7 @@ static void Setup_Preconditioner_EEM( const reax_system * const system,
if ( workspace->L == NULL )
{
if ( Allocate_Matrix( &(workspace->L_EEM), far_nbrs->n, fillin ) == FAILURE ||
Allocate_Matrix( &(workspace->U_EEM), far_nbrs->n, fillin ) == FAILURE ||
Allocate_Matrix( &(workspace->L), system->N_cm, fillin + system->N_cm ) == FAILURE ||
if ( Allocate_Matrix( &(workspace->L), system->N_cm, fillin + system->N_cm ) == FAILURE ||
Allocate_Matrix( &(workspace->U), system->N_cm, fillin + system->N_cm ) == FAILURE )
{
fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
......@@ -2150,9 +2220,7 @@ static void Setup_Preconditioner_EEM( const reax_system * const system,
if ( workspace->L == NULL )
{
/* factors have sparsity pattern as H */
if ( Allocate_Matrix( &(workspace->L_EEM), system->N, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->U_EEM), system->N, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->L), Hptr->n, Hptr->m ) == FAILURE ||
if ( Allocate_Matrix( &(workspace->L), Hptr->n, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->U), Hptr->n, Hptr->m ) == FAILURE )
{
fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
......@@ -2175,9 +2243,7 @@ static void Setup_Preconditioner_EEM( const reax_system * const system,
if ( workspace->L == NULL )
{
/* TODO: safest storage estimate is ILU(0) (same as lower triangular portion of H), could improve later */
if ( Allocate_Matrix( &(workspace->L_EEM), system->N, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->U_EEM), system->N, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->L), Hptr->n, Hptr->m ) == FAILURE ||
if ( Allocate_Matrix( &(workspace->L), Hptr->n, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->U), Hptr->n, Hptr->m ) == FAILURE )
{
fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
......@@ -2194,9 +2260,7 @@ static void Setup_Preconditioner_EEM( const reax_system * const system,
if ( workspace->L == NULL )
{
/* factors have sparsity pattern as H */
if ( Allocate_Matrix( &(workspace->L_EEM), system->N, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->U_EEM), system->N, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->L), Hptr->n, Hptr->m ) == FAILURE ||
if ( Allocate_Matrix( &(workspace->L), Hptr->n, Hptr->m ) == FAILURE ||
Allocate_Matrix( &(workspace->U), Hptr->n, Hptr->m ) == FAILURE )
{
fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
......@@ -2214,6 +2278,8 @@ static void Setup_Preconditioner_EEM( const reax_system * const system,
exit( INVALID_INPUT );
break;
}
Hptr->val[Hptr->start[system->N + 1] - 1] = 0.0;
}
......@@ -2244,25 +2310,11 @@ static void Setup_Preconditioner_ACKS2( const reax_system * const system,
{
Sort_Matrix_Rows( workspace->H_sp );
}
data->timing.cm_sort_mat_rows += Get_Timing_Info( time );
Hptr->val[Hptr->start[system->N + 1] - 1] = 1.0;
Hptr->val[Hptr->start[system->N_cm] - 1] = 1.0;
if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
{
if ( control->cm_domain_sparsify_enabled == TRUE )
{
Hptr = setup_graph_coloring( workspace->H_sp );
}
else
{
Hptr = setup_graph_coloring( workspace->H );
}
Sort_Matrix_Rows( Hptr );
}
data->timing.cm_sort_mat_rows += Get_Timing_Info( time );
#if defined(DEBUG)
fprintf( stderr, "H matrix sorted\n" );
#endif
......@@ -2397,13 +2449,19 @@ static void Calculate_Charges_QEq( const reax_system * const system,
for ( i = 0; i < system->N_cm; ++i )
{
system->atoms[i].q = workspace->s[0][i] - u * workspace->t[0][i];
#if defined(DEBUG_FOCUS)
printf("atom %4d: %f\n", i, system->atoms[i].q);
printf(" x[0]: %10.5f, x[1]: %10.5f, x[2]: %10.5f\n",
system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2]);
#endif
}
}
/* Get atomic charge q for EEM method
/* Get atomic charge q for EE method
*/
static void Calculate_Charges_EEM( const reax_system * const system,
static void Calculate_Charges_EE( const reax_system * const system,
static_storage * const workspace )
{
int i;
......@@ -2441,11 +2499,6 @@ static void QEq( reax_system * const system, control_params * const control,
Extrapolate_Charges_QEq( system, control, data, workspace );
// if( data->step == 0 || data->step == 100 )
// {
// Print_Linear_System( system, control, workspace, data->step );
// }
switch ( control->cm_solver_type )
{
case GMRES_S:
......@@ -2507,17 +2560,20 @@ static void QEq( reax_system * const system, control_params * const control,
Calculate_Charges_QEq( system, workspace );
//fprintf( stderr, "%d %.9f %.9f %.9f %.9f %.9f %.9f\n",
// data->step,
// workspace->s[0][0], workspace->t[0][0],
// workspace->s[0][1], workspace->t[0][1],
// workspace->s[0][2], workspace->t[0][2] );
// if( data->step == control->nsteps )
//Print_Charges( system, control, workspace, data->step );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "%d %.9f %.9f %.9f %.9f %.9f %.9f\n", data->step,
workspace->s[0][0], workspace->t[0][0],
workspace->s[0][1], workspace->t[0][1],
workspace->s[0][2], workspace->t[0][2] );
if( data->step == control->nsteps )
{
Print_Charges( system, control, workspace, data->step );
}
#endif
}
/* Main driver method for EEM kernel
/* Main driver method for EE kernel
*
* Rough outline:
* 1) init / setup routines for preconditioning of linear solver
......@@ -2526,7 +2582,7 @@ static void QEq( reax_system * const system, control_params * const control,
* 4) perform 1 linear solve
* 5) compute atomic charges based on output of (4)
*/
static void EEM( reax_system * const system, control_params * const control,
static void EE( reax_system * const system, control_params * const control,
simulation_data * const data, static_storage * const workspace,
const list * const far_nbrs, const output_controls * const out_control )
{
......@@ -2535,14 +2591,12 @@ static void EEM( reax_system * const system, control_params * const control,
if ( control->cm_solver_pre_comp_refactor > 0 &&
((data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) )
{
Setup_Preconditioner_EEM( system, control, data, workspace, far_nbrs );
Setup_Preconditioner_EE( system, control, data, workspace, far_nbrs );
Compute_Preconditioner_EEM( system, control, data, workspace, far_nbrs );
Compute_Preconditioner_EE( system, control, data, workspace, far_nbrs );
}
// Print_Linear_System( system, control, workspace, data->step );
Extrapolate_Charges_EEM( system, control, data, workspace );
Extrapolate_Charges_EE( system, control, data, workspace );
switch ( control->cm_solver_type )
{
......@@ -2571,7 +2625,7 @@ static void EEM( reax_system * const system, control_params * const control,
break;
default:
fprintf( stderr, "Unrecognized QEq solver selection. Terminating...\n" );
fprintf( stderr, "Unrecognized EE solver selection. Terminating...\n" );
exit( INVALID_INPUT );
break;
}
......@@ -2582,7 +2636,7 @@ static void EEM( reax_system * const system, control_params * const control,
fprintf( stderr, "linsolve-" );
#endif
Calculate_Charges_EEM( system, workspace );
Calculate_Charges_EE( system, workspace );
// if( data->step == control->nsteps )
//Print_Charges( system, control, workspace, data->step );
......@@ -2614,7 +2668,7 @@ static void ACKS2( reax_system * const system, control_params * const control,
// Print_Linear_System( system, control, workspace, data->step );
Extrapolate_Charges_EEM( system, control, data, workspace );
Extrapolate_Charges_EE( system, control, data, workspace );
switch ( control->cm_solver_type )
{
......@@ -2654,7 +2708,7 @@ static void ACKS2( reax_system * const system, control_params * const control,
fprintf( stderr, "linsolve-" );
#endif
Calculate_Charges_EEM( system, workspace );
Calculate_Charges_EE( system, workspace );
}
......@@ -2663,16 +2717,18 @@ void Compute_Charges( reax_system * const system, control_params * const control
const list * const far_nbrs, const output_controls * const out_control )
{
int i;
// char fname[200];
// FILE * fp;
#if defined(DEBUG_FOCUS)
char fname[200];
FILE * fp;
// if ( data->step == 10 || data->step == 50 || data->step == 100 )
// {
// sprintf( fname, "s_%d_%s.out", data->step, control->sim_name );
// fp = fopen( fname, "w" );
// Vector_Print( fp, NULL, workspace->s[0], system->N_cm );
// fclose( fp );
// }
if ( data->step == 0 || data->step == 10 || data->step == 50 || data->step == 100 )
{
sprintf( fname, "s_%d_%s.out", data->step, control->sim_name );
fp = fopen( fname, "w" );
Vector_Print( fp, NULL, workspace->s[0], system->N_cm );
fclose( fp );
}
#endif
switch ( control->charge_method )
{
......@@ -2680,8 +2736,8 @@ void Compute_Charges( reax_system * const system, control_params * const control
QEq( system, control, data, workspace, far_nbrs, out_control );
break;
case EEM_CM:
EEM( system, control, data, workspace, far_nbrs, out_control );
case EE_CM:
EE( system, control, data, workspace, far_nbrs, out_control );
break;
case ACKS2_CM:
......@@ -2694,13 +2750,20 @@ void Compute_Charges( reax_system * const system, control_params * const control
break;
}
// if ( data->step == 0 )
// {
// sprintf( fname, "H_%d_%s.out", data->step, control->sim_name );
// Print_Sparse_Matrix2( workspace->H, fname );
//
// sprintf( fname, "b_%d_%s.out", data->step, control->sim_name );
// fp = fopen( fname, "w" );
// Vector_Print( fp, NULL, workspace->b_s, system->N_cm );
// }
#if defined(DEBUG_FOCUS)
if ( data->step == 0 || data->step == 10 || data->step == 50 || data->step == 100 )
{
if ( data->step == 0 )
{
sprintf( fname, "H_%d_%s.out", data->step, control->sim_name );
Print_Sparse_Matrix2( workspace->H, fname, NULL );
Print_Sparse_Matrix_Binary( workspace->H, fname );
}
sprintf( fname, "b_%d_%s.out", data->step, control->sim_name );
fp = fopen( fname, "w" );
Vector_Print( fp, NULL, workspace->b_s, system->N_cm );
fclose( fp );
}
#endif
}
sPuReMD/src/forces.c
+ 5
− 4
View file @ 70d872fe
......@@ -310,7 +310,8 @@ static inline real Init_Charge_Matrix_Entry_Tab( reax_system *system,
}
break;
case EEM_CM:
case EE_CM:
//TODO
switch ( pos )
{
case OFF_DIAGONAL:
......@@ -388,7 +389,7 @@ static inline real Init_Charge_Matrix_Entry( reax_system *system,
}
break;
case EEM_CM:
case EE_CM:
switch ( pos )
{
case OFF_DIAGONAL:
......@@ -481,7 +482,7 @@ static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
case QEQ_CM:
break;
case EEM_CM:
case EE_CM:
H->start[system->N_cm - 1] = *Htop;
H_sp->start[system->N_cm - 1] = *H_sp_top;
......@@ -1203,7 +1204,7 @@ void Init_Forces_Tab( reax_system *system, control_params *control,
data->step, Htop, num_bonds, num_hbonds );
//Print_Bonds( system, bonds, "sbonds.out" );
//Print_Bond_List2( system, bonds, "sbonds.out" );
//Print_Sparse_Matrix2( H, "H.out" );
//Print_Sparse_Matrix2( H, "H.out", NULL );
#endif
}
......
sPuReMD/src/init_md.c
+ 3
− 12
View file @ 70d872fe
......@@ -298,7 +298,7 @@ void Init_Workspace( reax_system *system, control_params *control,
case QEQ_CM:
system->N_cm = system->N;
break;
case EEM_CM:
case EE_CM:
system->N_cm = system->N + 1;
break;
case ACKS2_CM:
......@@ -314,15 +314,6 @@ void Init_Workspace( reax_system *system, control_params *control,
workspace->H_sp = NULL;
workspace->L = NULL;
workspace->U = NULL;
workspace->H_EEM = NULL;
workspace->L_EEM = NULL;
workspace->U_EEM = NULL;
workspace->H_ACKS2_1 = NULL;
workspace->H_ACKS2_2 = NULL;
workspace->L_ACKS2_1 = NULL;
workspace->L_ACKS2_2 = NULL;
workspace->U_ACKS2_1 = NULL;
workspace->U_ACKS2_2 = NULL;
workspace->Hdia_inv = NULL;
if ( control->cm_solver_pre_comp_type == ICHOLT_PC ||
control->cm_solver_pre_comp_type == ILUT_PAR_PC )
......@@ -361,7 +352,7 @@ void Init_Workspace( reax_system *system, control_params *control,
}
break;
case EEM_CM:
case EE_CM:
for ( i = 0; i < system->N; ++i )
{
workspace->b_s[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
......@@ -535,7 +526,7 @@ void Init_Lists( reax_system *system, control_params *control,
case QEQ_CM:
max_nnz = Htop;
break;
case EEM_CM:
case EE_CM:
max_nnz = Htop + system->N_cm;
break;
case ACKS2_CM:
......
sPuReMD/src/mytypes.h
+ 1
− 5
View file @ 70d872fe
......@@ -193,7 +193,7 @@ enum geo_formats
enum charge_method
{
QEQ_CM = 0, EEM_CM = 1, ACKS2_CM = 2,
QEQ_CM = 0, EE_CM = 1, ACKS2_CM = 2,
};
enum solver
......@@ -781,10 +781,6 @@ typedef struct
/* charge method storage */
sparse_matrix *H, *H_sp, *L, *U;
/* EEM-specific */
sparse_matrix *H_EEM, *L_EEM, *U_EEM;
/* ACKS2-specific */
sparse_matrix *H_ACKS2_1, *H_ACKS2_2, *L_ACKS2_1, *L_ACKS2_2, *U_ACKS2_1, *U_ACKS2_2;
real *droptol;
real *w;
real *Hdia_inv;
......
sPuReMD/src/print_utils.c
+ 48
− 2
View file @ 70d872fe
......@@ -827,10 +827,19 @@ void Print_Sparse_Matrix( sparse_matrix *A )
}
void Print_Sparse_Matrix2( sparse_matrix *A, char *fname )
void Print_Sparse_Matrix2( sparse_matrix *A, char *fname, char *mode )
{
int i, j;
FILE *f = fopen( fname, "w" );
FILE *f;
if ( mode == NULL )
{
f = fopen( fname, "w" );
}
else
{
f = fopen( fname, mode );
}
for ( i = 0; i < A->n; ++i )
{
......@@ -846,6 +855,43 @@ void Print_Sparse_Matrix2( sparse_matrix *A, char *fname )
}
/* Note: watch out for portability issues with endianness
* due to serialization of numeric types (integer, IEEE 754) */
void Print_Sparse_Matrix_Binary( sparse_matrix *A, char *fname )
{
int i, j, temp;
FILE *f;
f = fopen( fname, "wb" );
/* header: # rows, # nonzeros */
fwrite( &(A->n), sizeof(unsigned int), 1, f );
fwrite( &(A->start[A->n]), sizeof(unsigned int), 1, f );
/* row pointers */
for ( i = 0; i <= A->n; ++i )
{
//Convert 0-based to 1-based (for Matlab)
temp = A->start[i] + 1;
fwrite( &temp, sizeof(unsigned int), 1, f );
}
/* column indices and non-zeros */
for ( i = 0; i <= A->n; ++i )
{
for ( j = A->start[i]; j < A->start[i + 1]; ++j )
{
//Convert 0-based to 1-based (for Matlab)
temp = A->j[j] + 1;
fwrite( &temp, sizeof(unsigned int), 1, f );
fwrite( &(A->val[j]), sizeof(real), 1, f );
}
}
fclose(f);
}
void Print_Bonds( reax_system *system, list *bonds, char *fname )
{
int i, pj;
......
sPuReMD/src/print_utils.h
+ 3
− 1
View file @ 70d872fe
......@@ -55,7 +55,9 @@ void Print_Soln( static_storage*, real*, real*, real*, int );
void Print_Sparse_Matrix( sparse_matrix* );
void Print_Sparse_Matrix2( sparse_matrix*, char* );
void Print_Sparse_Matrix2( sparse_matrix*, char*, char* );
void Print_Sparse_Matrix_Binary( sparse_matrix*, char* );
void Print_Bonds( reax_system*, list*, char* );
void Print_Bond_List2( reax_system*, list*, char* );
......
sPuReMD/src/vector.c
+ 1
− 1
View file @ 70d872fe
......@@ -114,7 +114,7 @@ inline void Vector_Add( real * const dest, const real c, const real * const v, c
void Vector_Print( FILE * const fout, const char * const vname, const real * const v,
const unsigned int k )
const unsigned int k )
{
unsigned int i;
......
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