forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10904 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
3285598d8d
commit
0f1efa0c79
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@ -0,0 +1,95 @@
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!BIOSYM archive 3
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PBC=ON
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Materials Studio Generated CAR File
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!DATE Sat Sep 28 14:53:25 2013
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||||
PBC 9.4214 18.8428 6.8814 90.0000 90.0000 90.0000 (P1)
|
||||
O1 -1.624219154 8.097696078 1.776747746 XXXX 1 o O -0.587
|
||||
O2 1.502039588 5.454548283 5.208548215 XXXX 1 o O -0.588
|
||||
O3 5.473135150 9.582203385 1.698707871 XXXX 1 o O -0.588
|
||||
O4 1.017177018 7.836457987 1.655336849 XXXX 1 o O -0.569
|
||||
O5 2.128465751 5.133975314 1.682995589 XXXX 1 o O -0.568
|
||||
O6 -3.906651937 8.881489521 5.078345256 XXXX 1 o O -0.569
|
||||
O7 -0.505405628 6.104981557 0.520103175 XXXX 1 o O -0.593
|
||||
O8 4.368060853 4.686240017 0.509230529 XXXX 1 o O -0.598
|
||||
O9 -3.159612633 6.680696169 3.970761259 XXXX 1 o O -0.593
|
||||
O10 -0.340215093 6.181566449 3.029805285 XXXX 1 o O -0.585
|
||||
O11 4.259096511 4.745758541 3.021092421 XXXX 1 o O -0.576
|
||||
O12 -3.202135223 6.888148742 6.479770697 XXXX 1 o O -0.586
|
||||
Ca1 -2.382573017 9.453046931 0.006968682 XXXX 1 ca+ Ca 1.255
|
||||
Ca2 -2.325796023 9.576218139 3.428878127 XXXX 1 ca+ Ca 1.254
|
||||
Ca3 -0.076380180 4.079881499 1.745044087 XXXX 1 ca+ Ca 1.217
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||||
Ca4 -5.921566269 10.257604097 5.121788234 XXXX 1 ca+ Ca 1.216
|
||||
Ca5 -1.211278300 6.053987274 5.191326594 XXXX 1 ca+ Ca 1.216
|
||||
P1 -0.385120417 7.101979887 1.743525377 XXXX 1 p P 0.480
|
||||
P2 3.460425980 4.274945926 1.740130960 XXXX 1 p P 0.481
|
||||
P3 -3.986908229 7.300465906 5.169344339 XXXX 1 p P 0.479
|
||||
O13 7.064357124 4.080776384 2.022615052 XXXX 1 o O -0.865
|
||||
H1 7.062035079 4.085255630 2.987706372 XXXX 1 ho H 0.266
|
||||
O14 6.334919154 0.061475662 5.217447746 XXXX 1 o O -0.587
|
||||
O15 3.208660412 2.704623456 1.767848215 XXXX 1 o O -0.588
|
||||
O16 -10.183835150 14.895311833 5.139407871 XXXX 1 o O -0.588
|
||||
O17 3.693522982 0.322713752 5.096036849 XXXX 1 o O -0.569
|
||||
O18 2.582234249 3.025196425 5.123695589 XXXX 1 o O -0.568
|
||||
O19 8.617351937 -0.722317782 1.637645256 XXXX 1 o O -0.569
|
||||
O20 5.216105628 2.054190182 3.960803175 XXXX 1 o O -0.593
|
||||
O21 0.342639147 3.472931722 3.949930529 XXXX 1 o O -0.598
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||||
O22 7.870312633 1.478475570 0.530061259 XXXX 1 o O -0.593
|
||||
O23 5.050915093 1.977605290 6.470505285 XXXX 1 o O -0.585
|
||||
O24 0.451603489 3.413413198 6.461792421 XXXX 1 o O -0.576
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O25 7.912835223 1.271022997 3.039070697 XXXX 1 o O -0.586
|
||||
Ca6 -2.328126983 15.024468286 3.447668682 XXXX 1 ca+ Ca 1.255
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Ca7 -2.384903977 14.901297078 6.869578127 XXXX 1 ca+ Ca 1.254
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Ca8 4.787080180 4.079290240 5.185744087 XXXX 1 ca+ Ca 1.217
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Ca9 1.210866269 14.219911120 1.681088234 XXXX 1 ca+ Ca 1.216
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Ca10 5.921978300 2.105184465 1.750626594 XXXX 1 ca+ Ca 1.216
|
||||
P4 5.095820417 1.057191852 5.184225377 XXXX 1 p P 0.480
|
||||
P5 1.250274020 3.884225813 5.180830960 XXXX 1 p P 0.481
|
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P6 8.697608229 0.858705833 1.728644339 XXXX 1 p P 0.479
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O26 -2.353657124 4.078395355 5.463315052 XXXX 1 o O -0.865
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H2 -2.351335079 4.073916109 6.428406372 XXXX 1 ho H 0.266
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O27 1.624219154 8.220647401 5.104652254 XXXX 1 o O -0.587
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O28 -1.502039588 10.863795195 1.672851785 XXXX 1 o O -0.588
|
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O29 -5.473135150 6.736140093 5.182692129 XXXX 1 o O -0.588
|
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O30 -1.017177018 8.481885491 5.226063151 XXXX 1 o O -0.569
|
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O31 -2.128465751 11.184368164 5.198404411 XXXX 1 o O -0.568
|
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O32 3.906651937 7.436853957 1.803054744 XXXX 1 o O -0.569
|
||||
O33 0.505405628 10.213361921 6.361296825 XXXX 1 o O -0.593
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O34 -4.368060853 11.632103462 6.372169471 XXXX 1 o O -0.598
|
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O35 3.159612633 9.637647309 2.910638741 XXXX 1 o O -0.593
|
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O36 0.340215093 10.136777029 3.851594715 XXXX 1 o O -0.585
|
||||
O37 -4.259096511 11.572584937 3.860307579 XXXX 1 o O -0.576
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O38 3.202135223 9.430194736 0.401629303 XXXX 1 o O -0.586
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Ca11 2.382573017 6.865296547 6.874431318 XXXX 1 ca+ Ca 1.255
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Ca12 2.325796023 6.742125339 3.452521873 XXXX 1 ca+ Ca 1.254
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Ca13 0.076380180 12.238461979 5.136355913 XXXX 1 ca+ Ca 1.217
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Ca14 5.921566269 6.060739381 1.759611766 XXXX 1 ca+ Ca 1.216
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Ca15 1.211278300 10.264356204 1.690073406 XXXX 1 ca+ Ca 1.216
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P7 0.385120417 9.216363591 5.137874623 XXXX 1 p P 0.480
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P8 -3.460425980 12.043397553 5.141269040 XXXX 1 p P 0.481
|
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P9 3.986908229 9.017877573 1.712055661 XXXX 1 p P 0.479
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O39 -7.064357124 12.237567095 4.858784948 XXXX 1 o O -0.865
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H3 -7.062035079 12.233087848 3.893693628 XXXX 1 ho H 0.266
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O40 -6.334919154 16.256867817 1.663952254 XXXX 1 o O -0.587
|
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O41 -3.208660412 13.613720023 5.113551785 XXXX 1 o O -0.588
|
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O42 10.183835150 1.423031646 1.741992129 XXXX 1 o O -0.588
|
||||
O43 -3.693522982 15.995629726 1.785363151 XXXX 1 o O -0.569
|
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O44 -2.582234249 13.293147054 1.757704411 XXXX 1 o O -0.568
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O45 -8.617351937 17.040661261 5.243754744 XXXX 1 o O -0.569
|
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O46 -5.216105628 14.264153297 2.920596825 XXXX 1 o O -0.593
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O47 -0.342639147 12.845411756 2.931469471 XXXX 1 o O -0.598
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O48 -7.870312633 14.839867909 6.351338741 XXXX 1 o O -0.593
|
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O49 -5.050915093 14.340738188 0.410894715 XXXX 1 o O -0.585
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O50 -0.451603489 12.904930280 0.419607579 XXXX 1 o O -0.576
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O51 -7.912835223 15.047320482 3.842329303 XXXX 1 o O -0.586
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Ca16 2.328126983 1.293875192 3.433731318 XXXX 1 ca+ Ca 1.255
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Ca17 2.384903977 1.417046400 0.011821873 XXXX 1 ca+ Ca 1.254
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Ca18 -4.787080180 12.239053239 1.695655913 XXXX 1 ca+ Ca 1.217
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Ca19 -1.210866269 2.098432358 5.200311766 XXXX 1 ca+ Ca 1.216
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Ca20 -5.921978300 14.213159014 5.130773406 XXXX 1 ca+ Ca 1.216
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P10 -5.095820417 15.261151626 1.697174623 XXXX 1 p P 0.480
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P11 -1.250274020 12.434117665 1.700569040 XXXX 1 p P 0.481
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P12 -8.697608229 15.459637645 5.152755661 XXXX 1 p P 0.479
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O52 2.353657124 12.239948123 1.418084948 XXXX 1 o O -0.865
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H4 2.351335079 12.244427370 0.452993628 XXXX 1 ho H 0.266
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end
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end
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@ -0,0 +1,116 @@
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!BIOSYM molecular_data 4
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!Date: Sat Sep 28 14:53:25 2013 Materials Studio Generated MDF file
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#topology
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@column 1 element
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@column 2 atom_type
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@column 3 charge_group
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@column 4 isotope
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@column 5 formal_charge
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@column 6 charge
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@column 7 switching_atom
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@column 8 oop_flag
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@column 9 chirality_flag
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@column 10 occupancy
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@column 11 xray_temp_factor
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@column 12 connections
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@molecule Molecule
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XXXX_1:O1 O o ? 0 1- -0.5867 0 0 8 1.0000 0.0000 P1
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XXXX_1:O2 O o ? 0 1- -0.5877 0 0 8 1.0000 0.0000 P5
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XXXX_1:O3 O o ? 0 1- -0.5880 0 0 8 1.0000 0.0000 P9
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XXXX_1:O4 O o ? 0 1- -0.5692 0 0 8 1.0000 0.0000 P1
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XXXX_1:O5 O o ? 0 1- -0.5678 0 0 8 1.0000 0.0000 P2
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XXXX_1:O6 O o ? 0 1- -0.5689 0 0 8 1.0000 0.0000 P3
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XXXX_1:O7 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P1
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XXXX_1:O8 O o ? 0 1- -0.5975 0 0 8 1.0000 0.0000 P2
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XXXX_1:O9 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P3
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XXXX_1:O10 O o ? 0 1- -0.5850 0 0 8 1.0000 0.0000 P1
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XXXX_1:O11 O o ? 0 1- -0.5761 0 0 8 1.0000 0.0000 P2
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XXXX_1:O12 O o ? 0 1- -0.5864 0 0 8 1.0000 0.0000 P3
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XXXX_1:Ca1 Ca ca+ ? 0 2+ 1.2549 0 0 8 1.0000 0.0000
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XXXX_1:Ca2 Ca ca+ ? 0 2+ 1.2543 0 0 8 1.0000 0.0000
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XXXX_1:Ca3 Ca ca+ ? 0 2+ 1.2171 0 0 8 1.0000 0.0000
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XXXX_1:Ca4 Ca ca+ ? 0 2+ 1.2161 0 0 8 1.0000 0.0000
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XXXX_1:Ca5 Ca ca+ ? 0 2+ 1.2165 0 0 8 1.0000 0.0000
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XXXX_1:P1 P p ? 0 1+ 0.4795 0 0 8 1.0000 0.0000 O4 O7 O1 O10
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XXXX_1:P2 P p ? 0 1+ 0.4810 0 0 8 1.0000 0.0000 O8 O15 O5 O11
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XXXX_1:P3 P p ? 0 1+ 0.4788 0 0 8 1.0000 0.0000 O12 O29 O6 O9
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XXXX_1:O13 O o ? 0 1- -0.8653 0 0 8 1.0000 0.0000 H1
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XXXX_1:H1 H ho ? 0 0 0.2657 0 0 8 1.0000 0.0000 O13
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XXXX_1:O14 O o ? 0 1- -0.5867 0 0 8 1.0000 0.0000 P4
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XXXX_1:O15 O o ? 0 1- -0.5877 0 0 8 1.0000 0.0000 P2
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XXXX_1:O16 O o ? 0 1- -0.5880 0 0 8 1.0000 0.0000 P12
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XXXX_1:O17 O o ? 0 1- -0.5692 0 0 8 1.0000 0.0000 P4
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XXXX_1:O18 O o ? 0 1- -0.5678 0 0 8 1.0000 0.0000 P5
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XXXX_1:O19 O o ? 0 1- -0.5689 0 0 8 1.0000 0.0000 P6
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XXXX_1:O20 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P4
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XXXX_1:O21 O o ? 0 1- -0.5975 0 0 8 1.0000 0.0000 P5
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XXXX_1:O22 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P6
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XXXX_1:O23 O o ? 0 1- -0.5850 0 0 8 1.0000 0.0000 P4
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XXXX_1:O24 O o ? 0 1- -0.5761 0 0 8 1.0000 0.0000 P5
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XXXX_1:O25 O o ? 0 1- -0.5864 0 0 8 1.0000 0.0000 P6
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XXXX_1:Ca6 Ca ca+ ? 0 2+ 1.2549 0 0 8 1.0000 0.0000
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||||
XXXX_1:Ca7 Ca ca+ ? 0 2+ 1.2543 0 0 8 1.0000 0.0000
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||||
XXXX_1:Ca8 Ca ca+ ? 0 2+ 1.2171 0 0 8 1.0000 0.0000
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XXXX_1:Ca9 Ca ca+ ? 0 2+ 1.2161 0 0 8 1.0000 0.0000
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XXXX_1:Ca10 Ca ca+ ? 0 2+ 1.2165 0 0 8 1.0000 0.0000
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XXXX_1:P4 P p ? 0 1+ 0.4795 0 0 8 1.0000 0.0000 O17 O20 O14 O23
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XXXX_1:P5 P p ? 0 1+ 0.4810 0 0 8 1.0000 0.0000 O21 O2 O18 O24
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XXXX_1:P6 P p ? 0 1+ 0.4788 0 0 8 1.0000 0.0000 O25 O42 O19 O22
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XXXX_1:O26 O o ? 0 1- -0.8653 0 0 8 1.0000 0.0000 H2
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XXXX_1:H2 H ho ? 0 0 0.2657 0 0 8 1.0000 0.0000 O26
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XXXX_1:O27 O o ? 0 1- -0.5867 0 0 8 1.0000 0.0000 P7
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||||
XXXX_1:O28 O o ? 0 1- -0.5877 0 0 8 1.0000 0.0000 P11
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||||
XXXX_1:O29 O o ? 0 1- -0.5880 0 0 8 1.0000 0.0000 P3
|
||||
XXXX_1:O30 O o ? 0 1- -0.5692 0 0 8 1.0000 0.0000 P7
|
||||
XXXX_1:O31 O o ? 0 1- -0.5678 0 0 8 1.0000 0.0000 P8
|
||||
XXXX_1:O32 O o ? 0 1- -0.5689 0 0 8 1.0000 0.0000 P9
|
||||
XXXX_1:O33 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P7
|
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XXXX_1:O34 O o ? 0 1- -0.5975 0 0 8 1.0000 0.0000 P8
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XXXX_1:O35 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P9
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XXXX_1:O36 O o ? 0 1- -0.5850 0 0 8 1.0000 0.0000 P7
|
||||
XXXX_1:O37 O o ? 0 1- -0.5761 0 0 8 1.0000 0.0000 P8
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XXXX_1:O38 O o ? 0 1- -0.5864 0 0 8 1.0000 0.0000 P9
|
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XXXX_1:Ca11 Ca ca+ ? 0 2+ 1.2549 0 0 8 1.0000 0.0000
|
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XXXX_1:Ca12 Ca ca+ ? 0 2+ 1.2543 0 0 8 1.0000 0.0000
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XXXX_1:Ca13 Ca ca+ ? 0 2+ 1.2171 0 0 8 1.0000 0.0000
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||||
XXXX_1:Ca14 Ca ca+ ? 0 2+ 1.2161 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca15 Ca ca+ ? 0 2+ 1.2165 0 0 8 1.0000 0.0000
|
||||
XXXX_1:P7 P p ? 0 1+ 0.4795 0 0 8 1.0000 0.0000 O30 O33 O27 O36
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||||
XXXX_1:P8 P p ? 0 1+ 0.4810 0 0 8 1.0000 0.0000 O34 O41 O31 O37
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||||
XXXX_1:P9 P p ? 0 1+ 0.4788 0 0 8 1.0000 0.0000 O38 O3 O32 O35
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XXXX_1:O39 O o ? 0 1- -0.8653 0 0 8 1.0000 0.0000 H3
|
||||
XXXX_1:H3 H ho ? 0 0 0.2657 0 0 8 1.0000 0.0000 O39
|
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XXXX_1:O40 O o ? 0 1- -0.5867 0 0 8 1.0000 0.0000 P10
|
||||
XXXX_1:O41 O o ? 0 1- -0.5877 0 0 8 1.0000 0.0000 P8
|
||||
XXXX_1:O42 O o ? 0 1- -0.5880 0 0 8 1.0000 0.0000 P6
|
||||
XXXX_1:O43 O o ? 0 1- -0.5692 0 0 8 1.0000 0.0000 P10
|
||||
XXXX_1:O44 O o ? 0 1- -0.5678 0 0 8 1.0000 0.0000 P11
|
||||
XXXX_1:O45 O o ? 0 1- -0.5689 0 0 8 1.0000 0.0000 P12
|
||||
XXXX_1:O46 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P10
|
||||
XXXX_1:O47 O o ? 0 1- -0.5975 0 0 8 1.0000 0.0000 P11
|
||||
XXXX_1:O48 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P12
|
||||
XXXX_1:O49 O o ? 0 1- -0.5850 0 0 8 1.0000 0.0000 P10
|
||||
XXXX_1:O50 O o ? 0 1- -0.5761 0 0 8 1.0000 0.0000 P11
|
||||
XXXX_1:O51 O o ? 0 1- -0.5864 0 0 8 1.0000 0.0000 P12
|
||||
XXXX_1:Ca16 Ca ca+ ? 0 2+ 1.2549 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca17 Ca ca+ ? 0 2+ 1.2543 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca18 Ca ca+ ? 0 2+ 1.2171 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca19 Ca ca+ ? 0 2+ 1.2161 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca20 Ca ca+ ? 0 2+ 1.2165 0 0 8 1.0000 0.0000
|
||||
XXXX_1:P10 P p ? 0 1+ 0.4795 0 0 8 1.0000 0.0000 O43 O46 O40 O49
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||||
XXXX_1:P11 P p ? 0 1+ 0.4810 0 0 8 1.0000 0.0000 O47 O28 O44 O50
|
||||
XXXX_1:P12 P p ? 0 1+ 0.4788 0 0 8 1.0000 0.0000 O51 O16 O45 O48
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||||
XXXX_1:O52 O o ? 0 1- -0.8653 0 0 8 1.0000 0.0000 H4
|
||||
XXXX_1:H4 H ho ? 0 0 0.2657 0 0 8 1.0000 0.0000 O52
|
||||
|
||||
!
|
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#symmetry
|
||||
@periodicity 3 xyz
|
||||
@group (P1)
|
||||
|
||||
#end
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||||
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@ -0,0 +1,95 @@
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!BIOSYM archive 3
|
||||
PBC=ON
|
||||
Materials Studio Generated CAR File
|
||||
!DATE Sat Sep 28 14:53:25 2013
|
||||
PBC 9.4214 18.8428 6.8814 90.0000 90.0000 90.0000 (P1)
|
||||
O1 -1.624219154 8.097696078 1.776747746 XXXX 1 o O -0.587
|
||||
O2 1.502039588 5.454548283 5.208548215 XXXX 1 o O -0.588
|
||||
O3 5.473135150 9.582203385 1.698707871 XXXX 1 o O -0.588
|
||||
O4 1.017177018 7.836457987 1.655336849 XXXX 1 o O -0.569
|
||||
O5 2.128465751 5.133975314 1.682995589 XXXX 1 o O -0.568
|
||||
O6 -3.906651937 8.881489521 5.078345256 XXXX 1 o O -0.569
|
||||
O7 -0.505405628 6.104981557 0.520103175 XXXX 1 o O -0.593
|
||||
O8 4.368060853 4.686240017 0.509230529 XXXX 1 o O -0.598
|
||||
O9 -3.159612633 6.680696169 3.970761259 XXXX 1 o O -0.593
|
||||
O10 -0.340215093 6.181566449 3.029805285 XXXX 1 o O -0.585
|
||||
O11 4.259096511 4.745758541 3.021092421 XXXX 1 o O -0.576
|
||||
O12 -3.202135223 6.888148742 6.479770697 XXXX 1 o O -0.586
|
||||
Ca1 -2.382573017 9.453046931 0.006968682 XXXX 1 ca+ Ca 1.255
|
||||
Ca2 -2.325796023 9.576218139 3.428878127 XXXX 1 ca+ Ca 1.254
|
||||
Ca3 -0.076380180 4.079881499 1.745044087 XXXX 1 ca+ Ca 1.217
|
||||
Ca4 -5.921566269 10.257604097 5.121788234 XXXX 1 ca+ Ca 1.216
|
||||
Ca5 -1.211278300 6.053987274 5.191326594 XXXX 1 ca+ Ca 1.216
|
||||
P1 -0.385120417 7.101979887 1.743525377 XXXX 1 p P 0.480
|
||||
P2 3.460425980 4.274945926 1.740130960 XXXX 1 p P 0.481
|
||||
P3 -3.986908229 7.300465906 5.169344339 XXXX 1 p P 0.479
|
||||
O13 7.064357124 4.080776384 2.022615052 XXXX 1 o O -0.865
|
||||
H1 7.062035079 4.085255630 2.987706372 XXXX 1 ho H 0.266
|
||||
O14 6.334919154 0.061475662 5.217447746 XXXX 1 o O -0.587
|
||||
O15 3.208660412 2.704623456 1.767848215 XXXX 1 o O -0.588
|
||||
O16 -10.183835150 14.895311833 5.139407871 XXXX 1 o O -0.588
|
||||
O17 3.693522982 0.322713752 5.096036849 XXXX 1 o O -0.569
|
||||
O18 2.582234249 3.025196425 5.123695589 XXXX 1 o O -0.568
|
||||
O19 8.617351937 -0.722317782 1.637645256 XXXX 1 o O -0.569
|
||||
O20 5.216105628 2.054190182 3.960803175 XXXX 1 o O -0.593
|
||||
O21 0.342639147 3.472931722 3.949930529 XXXX 1 o O -0.598
|
||||
O22 7.870312633 1.478475570 0.530061259 XXXX 1 o O -0.593
|
||||
O23 5.050915093 1.977605290 6.470505285 XXXX 1 o O -0.585
|
||||
O24 0.451603489 3.413413198 6.461792421 XXXX 1 o O -0.576
|
||||
O25 7.912835223 1.271022997 3.039070697 XXXX 1 o O -0.586
|
||||
Ca6 -2.328126983 15.024468286 3.447668682 XXXX 1 ca+ Ca 1.255
|
||||
Ca7 -2.384903977 14.901297078 6.869578127 XXXX 1 ca+ Ca 1.254
|
||||
Ca8 4.787080180 4.079290240 5.185744087 XXXX 1 ca+ Ca 1.217
|
||||
Ca9 1.210866269 14.219911120 1.681088234 XXXX 1 ca+ Ca 1.216
|
||||
Ca10 5.921978300 2.105184465 1.750626594 XXXX 1 ca+ Ca 1.216
|
||||
P4 5.095820417 1.057191852 5.184225377 XXXX 1 p P 0.480
|
||||
P5 1.250274020 3.884225813 5.180830960 XXXX 1 p P 0.481
|
||||
P6 8.697608229 0.858705833 1.728644339 XXXX 1 p P 0.479
|
||||
O26 -2.353657124 4.078395355 5.463315052 XXXX 1 o O -0.865
|
||||
H2 -2.351335079 4.073916109 6.428406372 XXXX 1 ho H 0.266
|
||||
O27 1.624219154 8.220647401 5.104652254 XXXX 1 o O -0.587
|
||||
O28 -1.502039588 10.863795195 1.672851785 XXXX 1 o O -0.588
|
||||
O29 -5.473135150 6.736140093 5.182692129 XXXX 1 o O -0.588
|
||||
O30 -1.017177018 8.481885491 5.226063151 XXXX 1 o O -0.569
|
||||
O31 -2.128465751 11.184368164 5.198404411 XXXX 1 o O -0.568
|
||||
O32 3.906651937 7.436853957 1.803054744 XXXX 1 o O -0.569
|
||||
O33 0.505405628 10.213361921 6.361296825 XXXX 1 o O -0.593
|
||||
O34 -4.368060853 11.632103462 6.372169471 XXXX 1 o O -0.598
|
||||
O35 3.159612633 9.637647309 2.910638741 XXXX 1 o O -0.593
|
||||
O36 0.340215093 10.136777029 3.851594715 XXXX 1 o O -0.585
|
||||
O37 -4.259096511 11.572584937 3.860307579 XXXX 1 o O -0.576
|
||||
O38 3.202135223 9.430194736 0.401629303 XXXX 1 o O -0.586
|
||||
Ca11 2.382573017 6.865296547 6.874431318 XXXX 1 ca+ Ca 1.255
|
||||
Ca12 2.325796023 6.742125339 3.452521873 XXXX 1 ca+ Ca 1.254
|
||||
Ca13 0.076380180 12.238461979 5.136355913 XXXX 1 ca+ Ca 1.217
|
||||
Ca14 5.921566269 6.060739381 1.759611766 XXXX 1 ca+ Ca 1.216
|
||||
Ca15 1.211278300 10.264356204 1.690073406 XXXX 1 ca+ Ca 1.216
|
||||
P7 0.385120417 9.216363591 5.137874623 XXXX 1 p P 0.480
|
||||
P8 -3.460425980 12.043397553 5.141269040 XXXX 1 p P 0.481
|
||||
P9 3.986908229 9.017877573 1.712055661 XXXX 1 p P 0.479
|
||||
O39 -7.064357124 12.237567095 4.858784948 XXXX 1 o O -0.865
|
||||
H3 -7.062035079 12.233087848 3.893693628 XXXX 1 ho H 0.266
|
||||
O40 -6.334919154 16.256867817 1.663952254 XXXX 1 o O -0.587
|
||||
O41 -3.208660412 13.613720023 5.113551785 XXXX 1 o O -0.588
|
||||
O42 10.183835150 1.423031646 1.741992129 XXXX 1 o O -0.588
|
||||
O43 -3.693522982 15.995629726 1.785363151 XXXX 1 o O -0.569
|
||||
O44 -2.582234249 13.293147054 1.757704411 XXXX 1 o O -0.568
|
||||
O45 -8.617351937 17.040661261 5.243754744 XXXX 1 o O -0.569
|
||||
O46 -5.216105628 14.264153297 2.920596825 XXXX 1 o O -0.593
|
||||
O47 -0.342639147 12.845411756 2.931469471 XXXX 1 o O -0.598
|
||||
O48 -7.870312633 14.839867909 6.351338741 XXXX 1 o O -0.593
|
||||
O49 -5.050915093 14.340738188 0.410894715 XXXX 1 o O -0.585
|
||||
O50 -0.451603489 12.904930280 0.419607579 XXXX 1 o O -0.576
|
||||
O51 -7.912835223 15.047320482 3.842329303 XXXX 1 o O -0.586
|
||||
Ca16 2.328126983 1.293875192 3.433731318 XXXX 1 ca+ Ca 1.255
|
||||
Ca17 2.384903977 1.417046400 0.011821873 XXXX 1 ca+ Ca 1.254
|
||||
Ca18 -4.787080180 12.239053239 1.695655913 XXXX 1 ca+ Ca 1.217
|
||||
Ca19 -1.210866269 2.098432358 5.200311766 XXXX 1 ca+ Ca 1.216
|
||||
Ca20 -5.921978300 14.213159014 5.130773406 XXXX 1 ca+ Ca 1.216
|
||||
P10 -5.095820417 15.261151626 1.697174623 XXXX 1 p P 0.480
|
||||
P11 -1.250274020 12.434117665 1.700569040 XXXX 1 p P 0.481
|
||||
P12 -8.697608229 15.459637645 5.152755661 XXXX 1 p P 0.479
|
||||
O52 2.353657124 12.239948123 1.418084948 XXXX 1 o O -0.865
|
||||
H4 2.351335079 12.244427370 0.452993628 XXXX 1 ho H 0.266
|
||||
end
|
||||
end
|
||||
|
|
@ -0,0 +1,116 @@
|
|||
!BIOSYM molecular_data 4
|
||||
|
||||
!Date: Sat Sep 28 14:53:25 2013 Materials Studio Generated MDF file
|
||||
|
||||
#topology
|
||||
|
||||
@column 1 element
|
||||
@column 2 atom_type
|
||||
@column 3 charge_group
|
||||
@column 4 isotope
|
||||
@column 5 formal_charge
|
||||
@column 6 charge
|
||||
@column 7 switching_atom
|
||||
@column 8 oop_flag
|
||||
@column 9 chirality_flag
|
||||
@column 10 occupancy
|
||||
@column 11 xray_temp_factor
|
||||
@column 12 connections
|
||||
|
||||
@molecule Molecule
|
||||
|
||||
XXXX_1:O1 O o ? 0 1- -0.5867 0 0 8 1.0000 0.0000 P1
|
||||
XXXX_1:O2 O o ? 0 1- -0.5877 0 0 8 1.0000 0.0000 P5
|
||||
XXXX_1:O3 O o ? 0 1- -0.5880 0 0 8 1.0000 0.0000 P9
|
||||
XXXX_1:O4 O o ? 0 1- -0.5692 0 0 8 1.0000 0.0000 P1
|
||||
XXXX_1:O5 O o ? 0 1- -0.5678 0 0 8 1.0000 0.0000 P2
|
||||
XXXX_1:O6 O o ? 0 1- -0.5689 0 0 8 1.0000 0.0000 P3
|
||||
XXXX_1:O7 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P1
|
||||
XXXX_1:O8 O o ? 0 1- -0.5975 0 0 8 1.0000 0.0000 P2
|
||||
XXXX_1:O9 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P3
|
||||
XXXX_1:O10 O o ? 0 1- -0.5850 0 0 8 1.0000 0.0000 P1
|
||||
XXXX_1:O11 O o ? 0 1- -0.5761 0 0 8 1.0000 0.0000 P2
|
||||
XXXX_1:O12 O o ? 0 1- -0.5864 0 0 8 1.0000 0.0000 P3
|
||||
XXXX_1:Ca1 Ca ca+ ? 0 2+ 1.2549 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca2 Ca ca+ ? 0 2+ 1.2543 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca3 Ca ca+ ? 0 2+ 1.2171 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca4 Ca ca+ ? 0 2+ 1.2161 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca5 Ca ca+ ? 0 2+ 1.2165 0 0 8 1.0000 0.0000
|
||||
XXXX_1:P1 P p ? 0 1+ 0.4795 0 0 8 1.0000 0.0000 O4 O7 O1 O10
|
||||
XXXX_1:P2 P p ? 0 1+ 0.4810 0 0 8 1.0000 0.0000 O8 O15 O5 O11
|
||||
XXXX_1:P3 P p ? 0 1+ 0.4788 0 0 8 1.0000 0.0000 O12 O29 O6 O9
|
||||
XXXX_1:O13 O o ? 0 1- -0.8653 0 0 8 1.0000 0.0000 H1
|
||||
XXXX_1:H1 H ho ? 0 0 0.2657 0 0 8 1.0000 0.0000 O13
|
||||
XXXX_1:O14 O o ? 0 1- -0.5867 0 0 8 1.0000 0.0000 P4
|
||||
XXXX_1:O15 O o ? 0 1- -0.5877 0 0 8 1.0000 0.0000 P2
|
||||
XXXX_1:O16 O o ? 0 1- -0.5880 0 0 8 1.0000 0.0000 P12
|
||||
XXXX_1:O17 O o ? 0 1- -0.5692 0 0 8 1.0000 0.0000 P4
|
||||
XXXX_1:O18 O o ? 0 1- -0.5678 0 0 8 1.0000 0.0000 P5
|
||||
XXXX_1:O19 O o ? 0 1- -0.5689 0 0 8 1.0000 0.0000 P6
|
||||
XXXX_1:O20 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P4
|
||||
XXXX_1:O21 O o ? 0 1- -0.5975 0 0 8 1.0000 0.0000 P5
|
||||
XXXX_1:O22 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P6
|
||||
XXXX_1:O23 O o ? 0 1- -0.5850 0 0 8 1.0000 0.0000 P4
|
||||
XXXX_1:O24 O o ? 0 1- -0.5761 0 0 8 1.0000 0.0000 P5
|
||||
XXXX_1:O25 O o ? 0 1- -0.5864 0 0 8 1.0000 0.0000 P6
|
||||
XXXX_1:Ca6 Ca ca+ ? 0 2+ 1.2549 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca7 Ca ca+ ? 0 2+ 1.2543 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca8 Ca ca+ ? 0 2+ 1.2171 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca9 Ca ca+ ? 0 2+ 1.2161 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca10 Ca ca+ ? 0 2+ 1.2165 0 0 8 1.0000 0.0000
|
||||
XXXX_1:P4 P p ? 0 1+ 0.4795 0 0 8 1.0000 0.0000 O17 O20 O14 O23
|
||||
XXXX_1:P5 P p ? 0 1+ 0.4810 0 0 8 1.0000 0.0000 O21 O2 O18 O24
|
||||
XXXX_1:P6 P p ? 0 1+ 0.4788 0 0 8 1.0000 0.0000 O25 O42 O19 O22
|
||||
XXXX_1:O26 O o ? 0 1- -0.8653 0 0 8 1.0000 0.0000 H2
|
||||
XXXX_1:H2 H ho ? 0 0 0.2657 0 0 8 1.0000 0.0000 O26
|
||||
XXXX_1:O27 O o ? 0 1- -0.5867 0 0 8 1.0000 0.0000 P7
|
||||
XXXX_1:O28 O o ? 0 1- -0.5877 0 0 8 1.0000 0.0000 P11
|
||||
XXXX_1:O29 O o ? 0 1- -0.5880 0 0 8 1.0000 0.0000 P3
|
||||
XXXX_1:O30 O o ? 0 1- -0.5692 0 0 8 1.0000 0.0000 P7
|
||||
XXXX_1:O31 O o ? 0 1- -0.5678 0 0 8 1.0000 0.0000 P8
|
||||
XXXX_1:O32 O o ? 0 1- -0.5689 0 0 8 1.0000 0.0000 P9
|
||||
XXXX_1:O33 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P7
|
||||
XXXX_1:O34 O o ? 0 1- -0.5975 0 0 8 1.0000 0.0000 P8
|
||||
XXXX_1:O35 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P9
|
||||
XXXX_1:O36 O o ? 0 1- -0.5850 0 0 8 1.0000 0.0000 P7
|
||||
XXXX_1:O37 O o ? 0 1- -0.5761 0 0 8 1.0000 0.0000 P8
|
||||
XXXX_1:O38 O o ? 0 1- -0.5864 0 0 8 1.0000 0.0000 P9
|
||||
XXXX_1:Ca11 Ca ca+ ? 0 2+ 1.2549 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca12 Ca ca+ ? 0 2+ 1.2543 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca13 Ca ca+ ? 0 2+ 1.2171 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca14 Ca ca+ ? 0 2+ 1.2161 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca15 Ca ca+ ? 0 2+ 1.2165 0 0 8 1.0000 0.0000
|
||||
XXXX_1:P7 P p ? 0 1+ 0.4795 0 0 8 1.0000 0.0000 O30 O33 O27 O36
|
||||
XXXX_1:P8 P p ? 0 1+ 0.4810 0 0 8 1.0000 0.0000 O34 O41 O31 O37
|
||||
XXXX_1:P9 P p ? 0 1+ 0.4788 0 0 8 1.0000 0.0000 O38 O3 O32 O35
|
||||
XXXX_1:O39 O o ? 0 1- -0.8653 0 0 8 1.0000 0.0000 H3
|
||||
XXXX_1:H3 H ho ? 0 0 0.2657 0 0 8 1.0000 0.0000 O39
|
||||
XXXX_1:O40 O o ? 0 1- -0.5867 0 0 8 1.0000 0.0000 P10
|
||||
XXXX_1:O41 O o ? 0 1- -0.5877 0 0 8 1.0000 0.0000 P8
|
||||
XXXX_1:O42 O o ? 0 1- -0.5880 0 0 8 1.0000 0.0000 P6
|
||||
XXXX_1:O43 O o ? 0 1- -0.5692 0 0 8 1.0000 0.0000 P10
|
||||
XXXX_1:O44 O o ? 0 1- -0.5678 0 0 8 1.0000 0.0000 P11
|
||||
XXXX_1:O45 O o ? 0 1- -0.5689 0 0 8 1.0000 0.0000 P12
|
||||
XXXX_1:O46 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P10
|
||||
XXXX_1:O47 O o ? 0 1- -0.5975 0 0 8 1.0000 0.0000 P11
|
||||
XXXX_1:O48 O o ? 0 1- -0.5926 0 0 8 1.0000 0.0000 P12
|
||||
XXXX_1:O49 O o ? 0 1- -0.5850 0 0 8 1.0000 0.0000 P10
|
||||
XXXX_1:O50 O o ? 0 1- -0.5761 0 0 8 1.0000 0.0000 P11
|
||||
XXXX_1:O51 O o ? 0 1- -0.5864 0 0 8 1.0000 0.0000 P12
|
||||
XXXX_1:Ca16 Ca ca+ ? 0 2+ 1.2549 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca17 Ca ca+ ? 0 2+ 1.2543 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca18 Ca ca+ ? 0 2+ 1.2171 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca19 Ca ca+ ? 0 2+ 1.2161 0 0 8 1.0000 0.0000
|
||||
XXXX_1:Ca20 Ca ca+ ? 0 2+ 1.2165 0 0 8 1.0000 0.0000
|
||||
XXXX_1:P10 P p ? 0 1+ 0.4795 0 0 8 1.0000 0.0000 O43 O46 O40 O49
|
||||
XXXX_1:P11 P p ? 0 1+ 0.4810 0 0 8 1.0000 0.0000 O47 O28 O44 O50
|
||||
XXXX_1:P12 P p ? 0 1+ 0.4788 0 0 8 1.0000 0.0000 O51 O16 O45 O48
|
||||
XXXX_1:O52 O o ? 0 1- -0.8653 0 0 8 1.0000 0.0000 H4
|
||||
XXXX_1:H4 H ho ? 0 0 0.2657 0 0 8 1.0000 0.0000 O52
|
||||
|
||||
!
|
||||
#symmetry
|
||||
@periodicity 3 xyz
|
||||
@group (P1)
|
||||
|
||||
#end
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
log log.hap_crystal-class1
|
||||
units real
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/cut 15.0
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data hap_crystal-class1.data
|
||||
|
||||
thermo_style multi
|
||||
minimize 0.0 0.0 100 1000
|
||||
|
||||
write_data hap_crystal-class1.data2
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
log log.hap_crystal-class2b
|
||||
units real
|
||||
atom_style full
|
||||
pair_style lj/class2/coul/cut 15.0
|
||||
bond_style class2
|
||||
angle_style class2
|
||||
improper_style class2
|
||||
|
||||
read_data hap_crystal-class2b.data
|
||||
|
||||
thermo_style multi
|
||||
minimize 0.0 0.0 100 1000
|
||||
|
||||
write_data hap_crystal-class2b.data2
|
||||
|
|
@ -1,6 +1,7 @@
|
|||
#!/bin/sh
|
||||
|
||||
MSI2LMP_LIBRARY=../frc_files
|
||||
VALGRIND='valgrind -v --track-origins=yes --show-reachable=yes --leak-check=full'
|
||||
MSI2LMP=../src/msi2lmp.exe
|
||||
LAMMPS=../../../src/lmp_serial
|
||||
CHECKDATA=./data-compare.pl
|
||||
|
|
@ -28,10 +29,12 @@ counter=0
|
|||
errors=0
|
||||
|
||||
# Class1 tests with cvff
|
||||
for m in hydrogen water h2-h2o ethane benzene naphthalene crambin nylon phen3_cff97
|
||||
for m in hydrogen water h2-h2o ethane benzene naphthalene crambin nylon phen3_cff97 hap_crystal
|
||||
do \
|
||||
before=$errors
|
||||
${MSI2LMP} ${m}-class1 -c 1 -p ${verbose} \
|
||||
vglog=${m}-class1.chk
|
||||
${VALGRIND} --log-file=${vglog} \
|
||||
${MSI2LMP} ${m}-class1 -c 1 -p ${verbose} \
|
||||
|| errors=$(expr $errors + 1)
|
||||
${LAMMPS} -log none -screen none -in in.${m}-class1 \
|
||||
|| errors=$(expr $errors + 1)
|
||||
|
|
@ -40,14 +43,23 @@ do \
|
|||
${CHECKDATA} ${m}-class1.data2 reference/${m}-class1.data2 \
|
||||
|| errors=$(expr $errors + 1)
|
||||
[ $before -eq $errors ] && rm ${m}-class1.data ${m}-class1.data2 log.${m}-class1
|
||||
counter=$(expr $counter + 4)
|
||||
leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog)
|
||||
[ $leak != 0 ] && echo "Memory still used: $leak" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog)
|
||||
[ $viol != 0 ] && echo "Valgrind errors: $viol" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
[ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog}
|
||||
counter=$(expr $counter + 6)
|
||||
done
|
||||
|
||||
# Class1 tests with clayff
|
||||
for m in PyAC_bulk
|
||||
do \
|
||||
before=$errors
|
||||
${MSI2LMP} ${m}-clayff -c 1 -p ${verbose} -f clayff -n \
|
||||
vglog=${m}-clayff.chk
|
||||
${VALGRIND} --log-file=${vglog} \
|
||||
${MSI2LMP} ${m}-clayff -c 1 -p ${verbose} -f clayff -n \
|
||||
|| errors=$(expr $errors + 1)
|
||||
${LAMMPS} -log none -screen none -in in.${m}-clayff \
|
||||
|| errors=$(expr $errors + 1)
|
||||
|
|
@ -56,14 +68,23 @@ do \
|
|||
${CHECKDATA} ${m}-clayff.data2 reference/${m}-clayff.data2 \
|
||||
|| errors=$(expr $errors + 1)
|
||||
[ $before -eq $errors ] && rm ${m}-clayff.data ${m}-clayff.data2 log.${m}-clayff
|
||||
counter=$(expr $counter + 4)
|
||||
leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog)
|
||||
[ $leak != 0 ] && echo "Memory still used: $leak" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog)
|
||||
[ $viol != 0 ] && echo "Valgrind errors: $viol" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
[ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog}
|
||||
counter=$(expr $counter + 6)
|
||||
done
|
||||
|
||||
# OPLS-AA tests
|
||||
for m in ethane
|
||||
do \
|
||||
before=$errors
|
||||
${MSI2LMP} ${m}-oplsaa -c 0 -p ${verbose} -f oplsaa -n \
|
||||
vglog=${m}-oplsaa.chk
|
||||
${VALGRIND} --log-file=${vglog} \
|
||||
${MSI2LMP} ${m}-oplsaa -c 0 -p ${verbose} -f oplsaa -n \
|
||||
|| errors=$(expr $errors + 1)
|
||||
${LAMMPS} -log none -screen none -in in.${m}-oplsaa \
|
||||
|| errors=$(expr $errors + 1)
|
||||
|
|
@ -72,14 +93,23 @@ do \
|
|||
${CHECKDATA} ${m}-oplsaa.data2 reference/${m}-oplsaa.data2 \
|
||||
|| errors=$(expr $errors + 1)
|
||||
[ $before -eq $errors ] && rm ${m}-oplsaa.data ${m}-oplsaa.data2 log.${m}-oplsaa
|
||||
counter=$(expr $counter + 4)
|
||||
leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog)
|
||||
[ $leak != 0 ] && echo "Memory still used: $leak" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog)
|
||||
[ $viol != 0 ] && echo "Valgrind errors: $viol" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
[ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog}
|
||||
counter=$(expr $counter + 6)
|
||||
done
|
||||
|
||||
# Class2 tests with compass
|
||||
for m in hydrogen ethane benzene naphthalene
|
||||
do \
|
||||
before=$errors
|
||||
${MSI2LMP} ${m}-class2a -c 2 -p ${verbose} -f compass_published \
|
||||
vglog=${m}-class2a.chk
|
||||
${VALGRIND} --log-file=${vglog} \
|
||||
${MSI2LMP} ${m}-class2a -c 2 -p ${verbose} -f compass_published \
|
||||
|| errors=$(expr $errors + 1)
|
||||
${LAMMPS} -log none -screen none -in in.${m}-class2a \
|
||||
|| errors=$(expr $errors + 1)
|
||||
|
|
@ -88,14 +118,23 @@ do \
|
|||
${CHECKDATA} ${m}-class2a.data2 reference/${m}-class2a.data2 \
|
||||
|| errors=$(expr $errors + 1)
|
||||
[ $before -eq $errors ] && rm ${m}-class2a.data ${m}-class2a.data2 log.${m}-class2a
|
||||
counter=$(expr $counter + 4)
|
||||
leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog)
|
||||
[ $leak != 0 ] && echo "Memory still used: $leak" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog)
|
||||
[ $viol != 0 ] && echo "Valgrind errors: $viol" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
[ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog}
|
||||
counter=$(expr $counter + 6)
|
||||
done
|
||||
|
||||
# Class2 tests with pcff
|
||||
for m in water h2-h2o ethane benzene naphthalene
|
||||
for m in water h2-h2o ethane benzene naphthalene hap_crystal
|
||||
do \
|
||||
before=$errors
|
||||
${MSI2LMP} ${m}-class2b -c 2 -p ${verbose} -f pcff \
|
||||
vglog=${m}-class2b.chk
|
||||
${VALGRIND} --log-file=${vglog} \
|
||||
${MSI2LMP} ${m}-class2b -c 2 -p ${verbose} -f pcff \
|
||||
|| errors=$(expr $errors + 1)
|
||||
${LAMMPS} -log none -screen none -in in.${m}-class2b \
|
||||
|| errors=$(expr $errors + 1)
|
||||
|
|
@ -104,7 +143,14 @@ do \
|
|||
${CHECKDATA} ${m}-class2b.data2 reference/${m}-class2b.data2 \
|
||||
|| errors=$(expr $errors + 1)
|
||||
[ $before -eq $errors ] && rm ${m}-class2b.data ${m}-class2b.data2 log.${m}-class2b
|
||||
counter=$(expr $counter + 4)
|
||||
leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog)
|
||||
[ $leak != 0 ] && echo "Memory still used: $leak" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog)
|
||||
[ $viol != 0 ] && echo "Valgrind errors: $viol" \
|
||||
&& errors=$(expr $errors + 1)
|
||||
[ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog}
|
||||
counter=$(expr $counter + 6)
|
||||
done
|
||||
|
||||
echo "Total error count: $errors / $counter"
|
||||
|
|
|
|||
Loading…
Reference in New Issue