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renormalize
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Lines changed: 50391 additions & 50391 deletions

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‎testsuite/MDAnalysisTests/data/adk_closed_NAMD.psf‎

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‎testsuite/MDAnalysisTests/data/gms/surf2wat.gms‎

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‎testsuite/MDAnalysisTests/data/gms/symopt.gms‎

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‎testsuite/MDAnalysisTests/data/gms/symopt.inp‎

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! EXAM 12.
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! This job illustrates linear bends, for acetylene.
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! The optimal RHF/STO-2G geometry is located.
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!
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! At the input geometry,
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! the FINAL E= -73.5036974734 after 7 iterations,
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! and the RMS gradient is 0.1506891.
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!
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! At the final geometry, 7 steps later,
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! the FINAL E= -73.6046483165, RMS gradient=0.0000028,
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! R(CC)=1.1777007 and R(CH)=1.0749435.
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!
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$CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE NZVAR=5 $END
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$SYSTEM TIMLIM=6 MEMORY=100000 $END
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$BASIS GBASIS=STO NGAUSS=2 $END
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$GUESS GUESS=HUCKEL $END
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$DATA
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Acetylene geometry optimization in internal coordinates
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Dnh 4
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CARBON 6.0 0.0 0.0 0.70
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HYDROGEN 1.0 0.0 0.0 1.78
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$END
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$ZMAT IZMAT(1)=1,1,2, 1,1,3, 1,2,4,
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5,1,2,4, 5,2,1,3 $END
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------- XZ is 1st plane for both bends -------
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$LIBE APTS(1)=1.0,0.0,0.0,1.0,0.0,0.0 $END
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! EXAM 12.
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! This job illustrates linear bends, for acetylene.
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! The optimal RHF/STO-2G geometry is located.
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!
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! At the input geometry,
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! the FINAL E= -73.5036974734 after 7 iterations,
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! and the RMS gradient is 0.1506891.
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!
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! At the final geometry, 7 steps later,
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! the FINAL E= -73.6046483165, RMS gradient=0.0000028,
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! R(CC)=1.1777007 and R(CH)=1.0749435.
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!
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$CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE NZVAR=5 $END
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$SYSTEM TIMLIM=6 MEMORY=100000 $END
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$BASIS GBASIS=STO NGAUSS=2 $END
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$GUESS GUESS=HUCKEL $END
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$DATA
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Acetylene geometry optimization in internal coordinates
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Dnh 4
20+
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CARBON 6.0 0.0 0.0 0.70
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HYDROGEN 1.0 0.0 0.0 1.78
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$END
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$ZMAT IZMAT(1)=1,1,2, 1,1,3, 1,2,4,
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5,1,2,4, 5,2,1,3 $END
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------- XZ is 1st plane for both bends -------
27+
$LIBE APTS(1)=1.0,0.0,0.0,1.0,0.0,0.0 $END

‎testsuite/MDAnalysisTests/data/mol2/BrokenMolecule.mol2‎

Lines changed: 13 additions & 13 deletions
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@<TRIPOS>MOLECULE
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FXA101_1
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49 51 1 0 0
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SMALL
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USER_CHARGES
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@<TRIPOS>ATOM
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@<TRIPOS>BOND
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@<TRIPOS>SUBSTRUCTURE
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1 Q101 19 GROUP 4 **** **** 0
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# MOE 2011.10 (io_trps.svl 2011.10)
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@<TRIPOS>MOLECULE
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FXA101_1
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49 51 1 0 0
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SMALL
5+
USER_CHARGES
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7+
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@<TRIPOS>ATOM
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@<TRIPOS>BOND
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@<TRIPOS>SUBSTRUCTURE
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1 Q101 19 GROUP 4 **** **** 0
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# MOE 2011.10 (io_trps.svl 2011.10)

‎testsuite/MDAnalysisTests/data/mol2/Molecule.mol2‎

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@<TRIPOS>MOLECULE
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FXA101_1
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49 51 1 0 0
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SMALL
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USER_CHARGES
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7-
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@<TRIPOS>ATOM
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1 N1 6.8420 9.9900 22.7430 N.am 1 Q101 -0.8960
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2 S1 8.1400 9.2310 23.3330 S.o2 1 Q101 1.3220
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3 N2 4.4000 9.1300 20.4710 N.am 1 Q101 -0.3970
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4 N3 3.0930 7.5030 14.2800 N.am 1 Q101 -0.4840
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5 O3 6.5760 8.3830 20.3400 O.2 1 Q101 -0.6040
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6 O4 2.6850 9.6850 14.3930 O.2 1 Q101 -0.6060
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7 C7 2.2280 7.4110 13.0930 C.3 1 Q101 0.0840
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8 C8 3.9480 6.3480 14.5990 C.3 1 Q101 0.0840
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9 C12 5.6510 9.2330 22.4370 C.3 1 Q101 0.1690
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10 C13 4.3540 10.0220 22.6400 C.3 1 Q101 -0.1080
19-
11 C14 3.4610 9.6140 21.4730 C.3 1 Q101 0.1020
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12 C15 4.0450 8.9850 19.0930 C.ar 1 Q101 0.0330
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13 C21 4.8560 9.4860 18.0840 C.ar 1 Q101 -0.1060
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14 C22 2.8610 8.3620 18.7270 C.ar 1 Q101 0.1210
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15 C24 4.5070 9.3620 16.7550 C.ar 1 Q101 -0.0920
24-
16 C26 2.4770 8.2190 17.4030 C.ar 1 Q101 -0.1400
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17 C27 3.3220 8.7250 16.4150 C.ar 1 Q101 -0.1150
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18 C28 3.0140 8.6530 14.9560 C.2 1 Q101 0.6760
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19 C50 5.6340 8.8540 20.9610 C.2 1 Q101 0.6950
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20 F1 2.0670 7.8840 19.6990 F 1 Q101 -0.1400
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21 O1 8.8810 10.2610 23.9930 O.2 1 Q101 -0.5930
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22 CL1 13.7140 7.5120 25.7230 Cl 1 Q101 -0.0550
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23 C1 12.0240 7.5430 26.0980 C.2 1 Q101 0.0330
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24 C2 11.4410 7.1410 27.2530 C.2 1 Q101 -0.1460
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25 S2 10.9140 8.1380 24.9280 S.3 1 Q101 0.0240
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26 C3 10.0540 7.3070 27.2020 C.2 1 Q101 -0.1130
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27 C4 9.5920 7.8360 26.0030 C.2 1 Q101 -0.0920
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28 C5 8.1780 8.0980 25.7100 C.2 1 Q101 0.0810
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29 C6 7.6020 8.0680 24.5090 C.2 1 Q101 -0.4200
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30 O2 8.6620 8.5580 22.1770 O.2 1 Q101 -0.5930
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31 H142 2.8750 10.4530 21.0840 H 1 Q101 0.0600
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32 H141 2.7930 8.7930 21.7530 H 1 Q101 0.0600
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33 H132 3.8910 9.8220 23.6100 H 1 Q101 0.0720
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34 H131 4.5540 11.1000 22.5880 H 1 Q101 0.0720
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35 H83 3.3600 5.6100 15.1400 H 1 Q101 0.0490
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36 H82 4.3320 5.9210 13.6680 H 1 Q101 0.0490
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37 H81 4.7860 6.6870 15.2030 H 1 Q101 0.0490
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38 H73 2.5530 8.1620 12.3690 H 1 Q101 0.0490
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39 H72 2.2830 6.4120 12.6530 H 1 Q101 0.0490
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40 H71 1.1920 7.6290 13.3750 H 1 Q101 0.0490
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41 H6 6.8360 7.3660 24.2130 H 1 Q101 0.1940
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42 H5 7.5750 8.2810 26.5990 H 1 Q101 0.1560
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43 H3 9.3940 7.0620 28.0290 H 1 Q101 0.1600
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44 H26 1.5500 7.7200 17.1560 H 1 Q101 0.1600
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45 H24 5.1410 9.7940 15.9920 H 1 Q101 0.1630
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46 H21 5.7800 10.0010 18.3330 H 1 Q101 0.1530
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47 H2 11.9710 6.7500 28.1100 H 1 Q101 0.1720
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48 H12 5.5880 8.2970 23.0050 H 1 Q101 0.0910
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49 H1 7.0200 10.8210 22.1720 H 1 Q101 0.4670
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@<TRIPOS>BOND
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1 1 2 am
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2 1 9 1
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3 1 49 1
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4 2 21 2
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5 2 29 1
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6 2 30 2
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7 3 11 1
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8 3 12 1
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9 3 19 am
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10 4 7 1
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11 4 8 1
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12 4 18 am
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13 5 19 2
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14 6 18 2
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15 7 38 1
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17 7 40 1
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23 9 48 1
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24 10 11 1
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25 10 33 1
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26 10 34 1
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27 11 31 1
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28 11 32 1
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29 12 13 ar
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30 12 14 ar
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31 13 15 ar
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32 13 46 1
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33 14 16 ar
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34 14 20 1
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35 15 17 ar
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36 15 45 1
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37 16 17 ar
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38 16 44 1
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39 17 18 1
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40 22 23 1
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41 23 24 2
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42 23 25 1
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43 24 26 1
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44 24 47 1
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45 25 27 1
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46 26 27 2
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50 28 42 1
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51 29 41 1
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@<TRIPOS>SUBSTRUCTURE
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1 Q101 19 GROUP 4 **** **** 0
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# MOE 2011.10 (io_trps.svl 2011.10)
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@<TRIPOS>MOLECULE
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FXA101_1
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49 51 1 0 0
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SMALL
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USER_CHARGES
6+
7+
8+
@<TRIPOS>ATOM
9+
1 N1 6.8420 9.9900 22.7430 N.am 1 Q101 -0.8960
10+
2 S1 8.1400 9.2310 23.3330 S.o2 1 Q101 1.3220
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3 N2 4.4000 9.1300 20.4710 N.am 1 Q101 -0.3970
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4 N3 3.0930 7.5030 14.2800 N.am 1 Q101 -0.4840
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5 O3 6.5760 8.3830 20.3400 O.2 1 Q101 -0.6040
14+
6 O4 2.6850 9.6850 14.3930 O.2 1 Q101 -0.6060
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7 C7 2.2280 7.4110 13.0930 C.3 1 Q101 0.0840
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8 C8 3.9480 6.3480 14.5990 C.3 1 Q101 0.0840
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9 C12 5.6510 9.2330 22.4370 C.3 1 Q101 0.1690
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10 C13 4.3540 10.0220 22.6400 C.3 1 Q101 -0.1080
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11 C14 3.4610 9.6140 21.4730 C.3 1 Q101 0.1020
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12 C15 4.0450 8.9850 19.0930 C.ar 1 Q101 0.0330
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13 C21 4.8560 9.4860 18.0840 C.ar 1 Q101 -0.1060
22+
14 C22 2.8610 8.3620 18.7270 C.ar 1 Q101 0.1210
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15 C24 4.5070 9.3620 16.7550 C.ar 1 Q101 -0.0920
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16 C26 2.4770 8.2190 17.4030 C.ar 1 Q101 -0.1400
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17 C27 3.3220 8.7250 16.4150 C.ar 1 Q101 -0.1150
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18 C28 3.0140 8.6530 14.9560 C.2 1 Q101 0.6760
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19 C50 5.6340 8.8540 20.9610 C.2 1 Q101 0.6950
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20 F1 2.0670 7.8840 19.6990 F 1 Q101 -0.1400
29+
21 O1 8.8810 10.2610 23.9930 O.2 1 Q101 -0.5930
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22 CL1 13.7140 7.5120 25.7230 Cl 1 Q101 -0.0550
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23 C1 12.0240 7.5430 26.0980 C.2 1 Q101 0.0330
32+
24 C2 11.4410 7.1410 27.2530 C.2 1 Q101 -0.1460
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25 S2 10.9140 8.1380 24.9280 S.3 1 Q101 0.0240
34+
26 C3 10.0540 7.3070 27.2020 C.2 1 Q101 -0.1130
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27 C4 9.5920 7.8360 26.0030 C.2 1 Q101 -0.0920
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28 C5 8.1780 8.0980 25.7100 C.2 1 Q101 0.0810
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29 C6 7.6020 8.0680 24.5090 C.2 1 Q101 -0.4200
38+
30 O2 8.6620 8.5580 22.1770 O.2 1 Q101 -0.5930
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31 H142 2.8750 10.4530 21.0840 H 1 Q101 0.0600
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32 H141 2.7930 8.7930 21.7530 H 1 Q101 0.0600
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33 H132 3.8910 9.8220 23.6100 H 1 Q101 0.0720
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34 H131 4.5540 11.1000 22.5880 H 1 Q101 0.0720
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35 H83 3.3600 5.6100 15.1400 H 1 Q101 0.0490
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36 H82 4.3320 5.9210 13.6680 H 1 Q101 0.0490
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37 H81 4.7860 6.6870 15.2030 H 1 Q101 0.0490
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38 H73 2.5530 8.1620 12.3690 H 1 Q101 0.0490
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39 H72 2.2830 6.4120 12.6530 H 1 Q101 0.0490
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40 H71 1.1920 7.6290 13.3750 H 1 Q101 0.0490
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41 H6 6.8360 7.3660 24.2130 H 1 Q101 0.1940
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42 H5 7.5750 8.2810 26.5990 H 1 Q101 0.1560
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43 H3 9.3940 7.0620 28.0290 H 1 Q101 0.1600
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44 H26 1.5500 7.7200 17.1560 H 1 Q101 0.1600
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45 H24 5.1410 9.7940 15.9920 H 1 Q101 0.1630
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46 H21 5.7800 10.0010 18.3330 H 1 Q101 0.1530
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47 H2 11.9710 6.7500 28.1100 H 1 Q101 0.1720
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48 H12 5.5880 8.2970 23.0050 H 1 Q101 0.0910
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49 H1 7.0200 10.8210 22.1720 H 1 Q101 0.4670
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@<TRIPOS>BOND
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1 1 2 am
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2 1 9 1
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3 1 49 1
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4 2 21 2
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5 2 29 1
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6 2 30 2
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29 12 13 ar
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32 13 46 1
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34 14 20 1
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46 26 27 2
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49 28 29 2
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50 28 42 1
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51 29 41 1
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@<TRIPOS>SUBSTRUCTURE
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1 Q101 19 GROUP 4 **** **** 0
112+
113+
# MOE 2011.10 (io_trps.svl 2011.10)

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