diff --git a/.gitignore b/.gitignore
index c07309633e9f7eb78b1f60a5ce45a617a8a79f8c..a24acea524b5f4ab694b591696d46cf7c6761af2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -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
diff --git a/data/benchmarks/water/ffield_Achtyl b/data/benchmarks/water/ffield_Achtyl
new file mode 100644
index 0000000000000000000000000000000000000000..ce54cb3bad2a701ff11a41f08679d98026a022d9
--- /dev/null
+++ b/data/benchmarks/water/ffield_Achtyl
@@ -0,0 +1,424 @@
+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
diff --git a/data/benchmarks/water/ffield_acks2.water b/data/benchmarks/water/ffield_acks2.water
new file mode 100644
index 0000000000000000000000000000000000000000..ddf2d3cbf5f8c76d3203ee4a326ee8db23fb246e
--- /dev/null
+++ b/data/benchmarks/water/ffield_acks2.water
@@ -0,0 +1,364 @@
+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
diff --git a/data/benchmarks/water/ffield_acks2_300.water b/data/benchmarks/water/ffield_acks2_300.water
new file mode 100644
index 0000000000000000000000000000000000000000..d4d7b7b94777b6c456acb5bc1ad1e40dcfaa4da0
--- /dev/null
+++ b/data/benchmarks/water/ffield_acks2_300.water
@@ -0,0 +1,364 @@
+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
diff --git a/environ/param.gpu.water b/environ/param.gpu.water
index 3c38e57dd9a357e3d293dcedc2e0becf90f15e72..c7aaf52d7be169df93420f640d4abe7d6ce1aba0 100644
--- a/environ/param.gpu.water
+++ b/environ/param.gpu.water
@@ -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
diff --git a/sPuReMD/src/charges.c b/sPuReMD/src/charges.c
index 54233396667390ad22f56163ceac981a645587c1..01279242f7a994bc9bd2f70b45a6742a45a2bde6 100644
--- a/sPuReMD/src/charges.c
+++ b/sPuReMD/src/charges.c
@@ -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
}
diff --git a/sPuReMD/src/forces.c b/sPuReMD/src/forces.c
index e6c82684a4ce4a5dcbc6b21d772cdd3b98015bfb..2d5e9a49e87d64b1dd0e4fdd439c9bb51f177c33 100644
--- a/sPuReMD/src/forces.c
+++ b/sPuReMD/src/forces.c
@@ -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
}
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index 4b93ec83c4d6dcfbb8c32ba2c7736889ba6fc635..4228f8bd4967cca1822e5d07fd0d5055503d5b20 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -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:
diff --git a/sPuReMD/src/mytypes.h b/sPuReMD/src/mytypes.h
index 7487086ec260f15f8731834ca444c02638365d17..b1090a2527aa879c00b1caa05c49839746bf87cf 100644
--- a/sPuReMD/src/mytypes.h
+++ b/sPuReMD/src/mytypes.h
@@ -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;
diff --git a/sPuReMD/src/print_utils.c b/sPuReMD/src/print_utils.c
index 8a5952760cd10372aa0ab548e0ed4886e85abfab..06b7d63dfbf0420a1b062ebc39a6c5bfee0f9234 100644
--- a/sPuReMD/src/print_utils.c
+++ b/sPuReMD/src/print_utils.c
@@ -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;
diff --git a/sPuReMD/src/print_utils.h b/sPuReMD/src/print_utils.h
index 8b3b363571ca5b7c50195b4c91bca8951c1caa7b..8c15ebbe81487eabf2a5db13627eef60ee8432d3 100644
--- a/sPuReMD/src/print_utils.h
+++ b/sPuReMD/src/print_utils.h
@@ -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* );
diff --git a/sPuReMD/src/vector.c b/sPuReMD/src/vector.c
index 483ba806d45432f9e2e0a0029d1db65058229cad..5cabd03b7f055ad02607eea052f5988c6ed2eaa3 100644
--- a/sPuReMD/src/vector.c
+++ b/sPuReMD/src/vector.c
@@ -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;