+
| + | KSR-2 | +IBM SP-2 | +
|---|---|---|
| +4 nodes + | ++4.0 + | ++ + | +
| +8 nodes + | ++8.1 + | ++ + | +
| +16 nodes + | ++15.1 + | ++ + | +
| +32 nodes + | ++24.7 + | ++ + | +
| +64 nodes + | ++33.3 + | ++ + | +
+
+ + + diff --git a/doc/nwahtml/nwargos_bmrks_drop.html b/doc/nwahtml/nwargos_bmrks_drop.html new file mode 100644 index 0000000000..9d266560b1 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_drop.html @@ -0,0 +1,158 @@ + +
nwARGOS drop benchmark
++
Molecular dynamics simulation of 216 SPC/E water molecules
+Timings are given for a molecular dynamics simulation of 216 SPC/E water molecules +subject to periodic boundary conditions, in the NVT ensemble. These timings were +obtained from simulations of 1000 steps, and reflect the wall-clock time of a +single molecular dynamics step. The setup time and time for periodic recording of +coordinates and velocities is not included. ++
| + | KSR-2 | +IBM SP-2 | +
|---|---|---|
| +4 nodes + | ++0.294088 + | ++ + | +
| +8 nodes + | ++0.165577 + | ++ + | +
| +16 nodes + | ++0.101206 + | ++ + | +
| +32 nodes + | ++0.110004 + | ++ + | +
| +64 nodes + | ++0.181529 + | ++ + | +
+Speedups relative to the 4 node timings +
| + | KSR-2 | +IBM SP-2 | +
|---|---|---|
| +4 nodes + | ++4.0 + | ++ + | +
| +8 nodes + | ++7.1 + | ++ + | +
| +16 nodes + | ++11.6 + | ++ + | +
| +32 nodes + | ++10.7 + | ++ + | +
| +64 nodes + | ++6.5 + | ++ + | +
+
+ + diff --git a/doc/nwahtml/nwargos_bmrks_ocean.html b/doc/nwahtml/nwargos_bmrks_ocean.html new file mode 100644 index 0000000000..ac2a709e1e --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_ocean.html @@ -0,0 +1,123 @@ + +
nwARGOS ocean benchmark
++
Molecular dynamics simulation of 27,000 SPC/E water molecules
+Timings are given for a molecular dynamics simulation of 27,000 SPC/E water molecules +subject to periodic boundary conditions, in the NVT ensemble. These timings were +obtained from simulations of 1000 steps, and reflect the wall-clock time of a +single molecular dynamics step. The setup time and time for periodic recording of +coordinates and velocities is not included. ++
| + | KSR-2 | +IBM SP-2 | +
|---|---|---|
| + | Rc=0.9 | +Rc=0.9 | +
| 4 nodes | ++ | 15.035754 | +
| 8 nodes | ++ | 7.290162 | +
| 20 nodes | ++ | 2.717282 | +
| 32 nodes | ++ | 2.766097 | +
| 50 nodes | ++ | 1.472683 | +
| 125 nodes | ++ | 1.107691 | +
+Speedups relative to the 4 node timings +
| + | KSR-2 | +IBM SP-2 | +
|---|---|---|
| + | Rc=0.9 | +Rc=0.9 | +
| 4 nodes | ++ | 4.0 | +
| 8 nodes | ++ | 8.3 | +
| 20 nodes | ++ | 22.1 | +
| 32 nodes | ++ | 21.7 | +
| 50 nodes | ++ | 40.8 | +
| 125 nodes | ++ | 54.3 | +
+
+ + + diff --git a/doc/nwahtml/nwargos_bmrks_river.html b/doc/nwahtml/nwargos_bmrks_river.html new file mode 100644 index 0000000000..d6f7978841 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_river.html @@ -0,0 +1,135 @@ + +
nwARGOS river benchmark
++
Molecular dynamics simulation of 5,832 SPC/E water molecules
+Timings are given for a molecular dynamics simulation of 5,832 SPC/E water molecules +subject to periodic boundary conditions, in the NVT ensemble. These timings were +obtained from simulations of 1000 steps, and reflect the wall-clock time of a +single molecular dynamics step. The setup time and time for periodic recording of +coordinates and velocities is not included. ++
| + | KSR-2 | +IBM SP-2 | +
|---|---|---|
| +4 nodes + | ++6.118019 + | ++3.023760 + | +
| +8 nodes + | ++2.866662 + | ++1.664759 + | +
| +27 nodes + | ++0.889270 + | ++ + | +
| +72 nodes + | ++0.408092 + | ++ + | +
+Speedups relative to the 4 node timings +
| + | KSR-2 | +IBM SP-2 | +
|---|---|---|
| +4 nodes + | ++4.0 + | ++4.0 + | +
| +8 nodes + | ++8.5 + | ++7.3 + | +
| +27 nodes + | ++27.5 + | ++ + | +
| +72 nodes + | ++60.0 + | ++ + | +
+
+ + + diff --git a/doc/nwahtml/nwargos_bmrks_sea.html b/doc/nwahtml/nwargos_bmrks_sea.html new file mode 100644 index 0000000000..ed09846ba1 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_sea.html @@ -0,0 +1,138 @@ + +
nwARGOS sea benchmark
++
Molecular dynamics simulation of 13,824 SPC/E water molecules
+Timings are given for a molecular dynamics simulation of 13,824 SPC/E water molecules +subject to periodic boundary conditions, in the NVT ensemble. These timings were +obtained from simulations of 1000 steps, and reflect the wall-clock time of a +single molecular dynamics step. The setup time and time for periodic recording of +coordinates and velocities is not included. ++
| + | KSR-2 | +IBM SP-2 | +IBM SP-2 | +
|---|---|---|---|
| + | Rc=0.9 | +Rc=0.9 | +Rc=1.8 | +
| 4 nodes | +15.117976 | +7.331969 | +52.237927 | +
| 8 nodes | +7.169106 | +3.816244 | +27.631083 | +
| 16 nodes | +3.472468 | +2.130735 | +13.496562 | +
| 32 nodes | +1.782187 | ++ | 6.811522 | +
| 64 nodes | +0.921344 | +1.007676 | +3.663068 | +
| 128 nodes | ++ | + | 2.280681 | +
+Speedups relative to the 4 node timings +
| + | KSR-2 | +IBM SP-2 | +|
|---|---|---|---|
| + | Rc=0.9 | +Rc=0.9 | +Rc=1.8 | +
| 4 nodes | +4.0 | +4.0 | +4.0 | +
| 8 nodes | +8.5 | +8.0 | +7.6 | +
| 16 nodes | +17.4 | +14.5 | +15.5 | +
| 32 nodes | +33.9 | +25.9 | +36.0 | +
| 64 nodes | +65.6 | +30.1 | +57.1 | +
| 128 nodes | ++ | + | 91.6 | +
+
+ + + diff --git a/doc/nwahtml/nwargos_bmrks_water_ksr.html b/doc/nwahtml/nwargos_bmrks_water_ksr.html new file mode 100644 index 0000000000..688eca5f4b --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_water_ksr.html @@ -0,0 +1,9 @@ + +
nwARGOS KSR-2 benchmarks
++
++ + diff --git a/doc/nwahtml/nwargos_bmrks_water_sp2.html b/doc/nwahtml/nwargos_bmrks_water_sp2.html new file mode 100644 index 0000000000..d7572c5141 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_water_sp2.html @@ -0,0 +1,9 @@ + +
nwARGOS IBM SP-2 benchmarks
++
++ + diff --git a/doc/nwahtml/nwargos_crown.html b/doc/nwahtml/nwargos_crown.html new file mode 100644 index 0000000000..9bf72be0ad --- /dev/null +++ b/doc/nwahtml/nwargos_crown.html @@ -0,0 +1,63 @@ + +
nwARGOS example: crown
++
+This example goes through the complete sequence of steps to perform a +free energy difference simulation in which Na+ is mutated into K+, +complexed to the crown ether 18C6, in aqueous solution. +
+
-
+
-
+The crown ether wil be built from CH2-O-CH2 fragments. This fragment
+is not part of the standard segment database. Also a corresponding fragment
+is not part of the fragment library. The fragment is created using an
+editor, and should be named
+coc_______.frg.
+
+
-
+The fragment just created is force field independent. To create the
+force field amber dependent segment file, give the command
+
+nwsgm coc_______ amber +
+This command searches the fragment libraries and the local file +coc_______.frg for a fragment entry $coc. +The generic atom types defined in the fragment are substituted for +the amber atom types. The translation tables are found in +the atom type translation library files or the local file +coc_______.att, if present. +A segment file coc_______.sgm +is created that should be renamed to crown.sgm. +Alternatively, this file may be appended to +amber_u.sgm or amber_r.sgm, provided that these library +files are defined in the file $HOME/.nwargos. +
+
-
+A sequence file needs to be created, defining the molecular system
+in terms of segments. Using an editor create the file
+crown.seq. This file defines
+the 18C6 crown ether in terms of six cyclicly arranged coc
+fragments. It also specifies the solvent as the SPC/E water model.
+
+
-
+The topology file crown.top is
+created, giving the command
+
+nwtop crown amber +
+This command searches the amber sequence database files, and +the local sequence file crown.seq for a sequence crown. +The force field needs to be given in order to search the correct +database files. If the sequence is found, it searches the amber +segment databases and the local segment file crown.sgm for all +segments specified in the sequence. When all segments have been found, +the topology is generated using the rules appropriate for the force +field. All parameters not explicitly given in the segment are added +from the amber parameter library files, and the local file +crown.par if present. Any segments or parameters not found +can be supplied in the local files. +
nwARGOS example: crown: coc fragment file
++
+
+$coc + 7 0 0 + 1C1 CT 1 0 1 1 0.000000 + 2H11 H1 0 0 1 1 0.150000 + 3H12 H1 0 0 1 1 0.150000 + 4O OS 0 0 1 1 -0.600000 + 5C2 CT 2 0 1 1 0.000000 + 6H21 H1 0 0 1 1 0.150000 + 7H22 H1 0 0 1 1 0.150000 + 1 4 5 + 2 1 3 + 6 5 7 ++
+
+Note that the first atom (C1) is defined as first link +atom, and the fifth atom (C2) is defined as second link +atom. + + diff --git a/doc/nwahtml/nwargos_crown_seq.html b/doc/nwahtml/nwargos_crown_seq.html new file mode 100644 index 0000000000..0d475fed2e --- /dev/null +++ b/doc/nwahtml/nwargos_crown_seq.html @@ -0,0 +1,29 @@ + +
nwARGOS example: crown: sequence file
++
+
+$crown + 1coc + 2coc + 3coc + 4coc + 5coc + 6coc 0 0 1 1 + -2 + 0SPCE + -3 ++
+
+Note that the sixth coc segment's second link is pointing +to the first link atom of the first coc segment, to make +the cyclic crown ether. Alternatively this could have been specified +by letting the first coc segment's first link point to the +sixth coc segment's second link atom. The other coc +segments are automatically link their first link atom to their previous +segment's second link atom. + + diff --git a/doc/nwahtml/nwargos_crown_sgm.html b/doc/nwahtml/nwargos_crown_sgm.html new file mode 100644 index 0000000000..dd7d328b33 --- /dev/null +++ b/doc/nwahtml/nwargos_crown_sgm.html @@ -0,0 +1,62 @@ + +
nwARGOS example: crown: coc fragment file
++
+
+$coc + 7 6 7 4 0 + 1C1 CT CT CT 1 1 1 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 2H11 H H H 1 1 0 0 + 0.150000 0.000000 0.150000 0.000000 0.150000 0.000000 + 3H12 H H H 1 1 0 0 + 0.150000 0.000000 0.150000 0.000000 0.150000 0.000000 + 4O O O O 1 1 0 0 + -0.600000 0.000000 -0.600000 0.000000 -0.600000 0.000000 + 5C2 CT CT CT 1 1 2 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6H21 H H H 1 1 0 0 + 0.150000 0.000000 0.150000 0.000000 0.150000 0.000000 + 7H22 H H H 1 1 0 0 + 0.150000 0.000000 0.150000 0.000000 0.150000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 5 5 6 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 6 5 7 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 4 1 4 5 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 5 4 5 6 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 6 4 5 7 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 7 6 5 7 0 0 + 0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00 + 1 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 + 2 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 + 3 1 4 5 6 0 0 + 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 + 4 1 4 5 7 0 0 + 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 ++
+
+ + diff --git a/doc/nwahtml/nwargos_crown_top.html b/doc/nwahtml/nwargos_crown_top.html new file mode 100644 index 0000000000..d153aae2aa --- /dev/null +++ b/doc/nwahtml/nwargos_crown_top.html @@ -0,0 +1,665 @@ + +
nwARGOS example: crown: topology file
++
+
+nwArgos test topology + generated by nwtop + test + 0 amber + 5 +OW w 15.999400OW w 15.999400OW w 15.999400 +HW w 1.008000HW w 1.008000HW w 1.008000 +CT 12.011000CT 12.011000CT 12.011000 +H2 1.007940H2 1.007940H2 1.007940 +OS 15.999400OS 15.999400OS 15.999400 + 0.24887E-02 0.24887E-02 0.24887E-02 0.12444E-02 0.12444E-02 0.12444E-02 + 0.24348E-05 0.24348E-05 0.24348E-05 0.12174E-05 0.12174E-05 0.12174E-05 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.26639E-02 0.26639E-02 0.26639E-02 0.13319E-02 0.13319E-02 0.13319E-02 + 0.32882E-05 0.32882E-05 0.32882E-05 0.16441E-05 0.16441E-05 0.16441E-05 + 0.33252E-03 0.33252E-03 0.33252E-03 0.16626E-03 0.16626E-03 0.16626E-03 + 0.13524E-06 0.13524E-06 0.13524E-06 0.67620E-07 0.67620E-07 0.67620E-07 + 0.22764E-02 0.22764E-02 0.22764E-02 0.11382E-02 0.11382E-02 0.11382E-02 + 0.19260E-05 0.19260E-05 0.19260E-05 0.96298E-06 0.96298E-06 0.96298E-06 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + 0.28268E-02 0.28268E-02 0.28268E-02 0.14134E-02 0.14134E-02 0.14134E-02 + 0.43642E-05 0.43642E-05 0.43642E-05 0.21821E-05 0.21821E-05 0.21821E-05 + 0.36890E-03 0.36890E-03 0.36890E-03 0.18445E-03 0.18445E-03 0.18445E-03 + 0.19620E-06 0.19620E-06 0.19620E-06 0.98100E-07 0.98100E-07 0.98100E-07 + 0.24503E-02 0.24503E-02 0.24503E-02 0.12251E-02 0.12251E-02 0.12251E-02 + 0.26302E-05 0.26302E-05 0.26302E-05 0.13151E-05 0.13151E-05 0.13151E-05 + 0.38210E-04 0.38210E-04 0.38210E-04 0.19105E-04 0.19105E-04 0.19105E-04 + 0.55564E-08 0.55564E-08 0.55564E-08 0.27782E-08 0.27782E-08 0.27782E-08 + 0.29717E-03 0.29717E-03 0.29717E-03 0.14859E-03 0.14859E-03 0.14859E-03 + 0.10213E-06 0.10213E-06 0.10213E-06 0.51063E-07 0.51063E-07 0.51063E-07 + 0.20747E-02 0.20747E-02 0.20747E-02 0.10374E-02 0.10374E-02 0.10374E-02 + 0.15125E-05 0.15125E-05 0.15125E-05 0.75626E-06 0.75626E-06 0.75626E-06 + 3 3 0 0 0 0 0 + 42 42 78 108 0 90 210 + 1 0 0 0 0SPCE MOW 1 + -0.847600 -0.847600 -0.847600 0.000000 0.000000 0.000000 + 2 0 0 0 0SPCE MHW 2 + 0.423800 0.423800 0.423800 0.000000 0.000000 0.000000 + 2 0 0 0 0SPCE MHW 3 + 0.423800 0.423800 0.423800 0.000000 0.000000 0.000000 + 1 2 1 1 + 0.100000 0.00000E+00 0.100000 0.00000E+00 0.100000 0.00000E+00 + 1 3 1 2 + 0.100000 0.00000E+00 0.100000 0.00000E+00 0.100000 0.00000E+00 + 2 3 1 3 + 0.163333 0.00000E+00 0.163333 0.00000E+00 0.163333 0.00000E+00 + 3 1 1 1 1coc C1 1 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 1 1 1coc H11 2 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 1 1 1coc H12 3 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 5 1 1 1 1coc O 4 0 + -0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000 + 3 1 1 1 1coc C2 5 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 1 1 1coc H21 6 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 1 1 1coc H22 7 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 3 1 2 2 2coc C1 8 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 2 2 2coc H11 9 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 2 2 2coc H12 10 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 5 1 2 2 2coc O 11 0 + -0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000 + 3 1 2 2 2coc C2 12 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 2 2 2coc H21 13 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 2 2 2coc H22 14 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 3 1 3 3 3coc C1 15 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 3 3 3coc H11 16 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 3 3 3coc H12 17 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 5 1 3 3 3coc O 18 0 + -0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000 + 3 1 3 3 3coc C2 19 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 3 3 3coc H21 20 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 3 3 3coc H22 21 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 3 1 4 4 4coc C1 22 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 4 4 4coc H11 23 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 4 4 4coc H12 24 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 5 1 4 4 4coc O 25 0 + -0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000 + 3 1 4 4 4coc C2 26 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 4 4 4coc H21 27 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 4 4 4coc H22 28 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 3 1 5 5 5coc C1 29 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 5 5 5coc H11 30 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 5 5 5coc H12 31 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 5 1 5 5 5coc O 32 0 + -0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000 + 3 1 5 5 5coc C2 33 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 5 5 5coc H21 34 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 5 5 5coc H22 35 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 3 1 6 6 6coc C1 36 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 6 6 6coc H11 37 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 6 6 6coc H12 38 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 5 1 6 6 6coc O 39 0 + -0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000 + 3 1 6 6 6coc C2 40 0 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 1 6 6 6coc H21 41 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 4 1 6 6 6coc H22 42 0 + 0.150000 0.150000 0.150000 0.000000 0.000000 0.000000 + 1 2 1 1 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 1 3 1 2 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 1 4 0 3 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 4 5 0 4 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 5 6 1 5 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 5 7 1 6 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 8 9 1 7 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 8 10 1 8 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 8 11 0 9 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 11 12 0 10 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 12 13 1 11 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 12 14 1 12 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 8 5 0 13 + 0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06 + 15 16 1 14 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 15 17 1 15 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 15 18 0 16 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 18 19 0 17 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 19 20 1 18 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 19 21 1 19 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 15 12 0 20 + 0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06 + 22 23 1 21 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 22 24 1 22 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 22 25 0 23 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 25 26 0 24 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 26 27 1 25 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 26 28 1 26 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 22 19 0 27 + 0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06 + 29 30 1 28 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 29 31 1 29 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 29 32 0 30 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 32 33 0 31 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 33 34 1 32 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 33 35 1 33 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 29 26 0 34 + 0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06 + 36 37 1 35 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 36 38 1 36 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 36 39 0 37 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 39 40 0 38 + 0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06 + 40 41 1 39 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 40 42 1 40 + 0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06 + 36 33 0 41 + 0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06 + 40 1 0 42 + 0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06 + 2 1 3 0 1 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 2 1 4 0 2 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 3 1 4 0 3 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 1 4 5 0 4 + 1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03 + 4 5 6 0 5 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 4 5 7 0 6 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 6 5 7 0 7 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 9 8 10 0 8 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 9 8 11 0 9 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 10 8 11 0 10 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 8 11 12 0 11 + 1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03 + 11 12 13 0 12 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 11 12 14 0 13 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 13 12 14 0 14 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 9 8 5 0 15 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 10 8 5 0 16 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 11 8 5 0 17 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 4 5 8 0 18 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 6 5 8 0 19 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 7 5 8 0 20 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 16 15 17 0 21 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 16 15 18 0 22 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 17 15 18 0 23 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 15 18 19 0 24 + 1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03 + 18 19 20 0 25 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 18 19 21 0 26 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 20 19 21 0 27 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 16 15 12 0 28 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 17 15 12 0 29 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 18 15 12 0 30 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 11 12 15 0 31 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 13 12 15 0 32 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 14 12 15 0 33 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 23 22 24 0 34 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 23 22 25 0 35 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 24 22 25 0 36 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 22 25 26 0 37 + 1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03 + 25 26 27 0 38 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 25 26 28 0 39 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 27 26 28 0 40 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 23 22 19 0 41 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 24 22 19 0 42 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 25 22 19 0 43 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 18 19 22 0 44 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 20 19 22 0 45 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 21 19 22 0 46 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 30 29 31 0 47 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 30 29 32 0 48 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 31 29 32 0 49 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 29 32 33 0 50 + 1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03 + 32 33 34 0 51 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 32 33 35 0 52 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 34 33 35 0 53 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 30 29 26 0 54 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 31 29 26 0 55 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 32 29 26 0 56 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 25 26 29 0 57 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 27 26 29 0 58 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 28 26 29 0 59 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 37 36 38 0 60 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 37 36 39 0 61 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 38 36 39 0 62 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 36 39 40 0 63 + 1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03 + 39 40 41 0 64 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 39 40 42 0 65 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 41 40 42 0 66 + 1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03 + 37 36 33 0 67 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 38 36 33 0 68 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 39 36 33 0 69 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 32 33 36 0 70 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 34 33 36 0 71 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 35 33 36 0 72 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 39 40 1 0 73 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 41 40 1 0 74 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 42 40 1 0 75 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 2 1 40 0 76 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 3 1 40 0 77 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 4 1 40 0 78 + 1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03 + 2 1 4 5 0 1 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 3 1 4 5 0 2 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 1 4 5 6 0 3 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 1 4 5 7 0 4 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 9 8 11 12 0 5 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 10 8 11 12 0 6 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 8 11 12 13 0 7 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 8 11 12 14 0 8 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 4 5 8 9 0 9 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 6 5 8 9 0 10 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 7 5 8 9 0 11 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 4 5 8 10 0 12 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 6 5 8 10 0 13 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 7 5 8 10 0 14 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 5 8 11 12 0 15 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 5 8 11 12 0 15 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 4 5 8 11 0 16 + 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 + 4 5 8 11 0 16 + 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 + 6 5 8 11 0 17 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 7 5 8 11 0 18 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 1 4 5 8 0 19 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 1 4 5 8 0 19 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 40 1 4 5 0 20 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 40 1 4 5 0 20 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 16 15 18 19 0 21 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 17 15 18 19 0 22 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 15 18 19 20 0 23 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 15 18 19 21 0 24 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 11 12 15 16 0 25 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 13 12 15 16 0 26 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 14 12 15 16 0 27 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 11 12 15 17 0 28 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 13 12 15 17 0 29 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 14 12 15 17 0 30 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 12 15 18 19 0 31 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 12 15 18 19 0 31 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 11 12 15 18 0 32 + 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 + 11 12 15 18 0 32 + 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 + 13 12 15 18 0 33 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 14 12 15 18 0 34 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 8 11 12 15 0 35 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 8 11 12 15 0 35 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 23 22 25 26 0 36 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 24 22 25 26 0 37 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 22 25 26 27 0 38 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 22 25 26 28 0 39 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 18 19 22 23 0 40 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 20 19 22 23 0 41 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 21 19 22 23 0 42 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 18 19 22 24 0 43 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 20 19 22 24 0 44 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 21 19 22 24 0 45 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 19 22 25 26 0 46 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 19 22 25 26 0 46 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 18 19 22 25 0 47 + 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 + 18 19 22 25 0 47 + 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 + 20 19 22 25 0 48 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 21 19 22 25 0 49 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 15 18 19 22 0 50 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 15 18 19 22 0 50 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 30 29 32 33 0 51 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 31 29 32 33 0 52 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 29 32 33 34 0 53 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 29 32 33 35 0 54 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 25 26 29 30 0 55 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 27 26 29 30 0 56 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 28 26 29 30 0 57 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 25 26 29 31 0 58 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 27 26 29 31 0 59 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 28 26 29 31 0 60 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 25 26 29 32 0 61 + 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 + 25 26 29 32 0 61 + 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 + 27 26 29 32 0 62 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 28 26 29 32 0 63 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 26 29 32 33 0 64 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 26 29 32 33 0 64 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 22 25 26 29 0 65 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 22 25 26 29 0 65 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 37 36 39 40 0 66 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 38 36 39 40 0 67 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 36 39 40 41 0 68 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 36 39 40 42 0 69 + 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 + 32 33 36 37 0 70 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 34 33 36 37 0 71 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 35 33 36 37 0 72 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 32 33 36 38 0 73 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 34 33 36 38 0 74 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 35 33 36 38 0 75 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 32 33 36 39 0 76 + 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 + 32 33 36 39 0 76 + 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 + 34 33 36 39 0 77 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 35 33 36 39 0 78 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 33 36 39 40 0 79 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 33 36 39 40 0 79 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 1 4 5 8 0 80 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 1 4 5 8 0 80 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 2 1 40 39 0 81 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 3 1 40 39 0 82 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 4 1 40 39 0 83 + 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 + 4 1 40 39 0 83 + 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 + 2 1 40 41 0 84 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 3 1 40 41 0 85 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 4 1 40 41 0 86 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 2 1 40 42 0 87 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 3 1 40 42 0 88 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 4 1 40 42 0 89 + 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 + 40 1 4 5 0 90 + 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 + 40 1 4 5 0 90 + 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 + 1 1 1 1 2 2 2 2 3 3 3 + 3 4 4 4 4 4 4 5 5 6 6 + 6 7 7 7 8 8 8 9 10 11 11 + 11 12 13 13 13 14 14 14 15 15 15 + 16 17 18 18 18 19 20 20 20 21 21 + 21 22 22 22 23 24 25 25 25 26 27 + 27 27 28 28 28 29 29 29 30 31 32 + 32 32 33 34 34 34 35 35 35 36 36 + 37 38 + 6 7 8 36 5 39 41 42 5 39 41 + 42 9 10 11 39 41 42 12 40 9 10 + 11 9 10 11 13 14 15 12 12 16 17 + 18 19 16 17 18 16 17 18 20 21 22 + 19 19 23 24 25 26 23 24 25 23 24 + 25 27 28 29 26 26 30 31 32 33 30 + 31 32 30 31 32 34 35 36 33 33 37 + 38 39 40 37 38 39 37 38 39 41 42 + 40 40 + 1 1 1 1 1 1 1 1 2 2 2 + 2 2 2 2 3 3 3 3 3 3 4 + 4 4 4 4 4 4 4 4 4 4 5 + 5 5 5 6 6 6 6 6 7 7 7 + 7 8 8 8 8 8 8 8 8 9 9 + 9 9 10 10 10 11 11 11 11 11 11 + 11 11 12 12 12 13 13 13 13 13 14 + 14 14 14 15 15 15 15 15 15 15 15 + 16 16 16 16 17 17 17 18 18 18 18 + 18 18 18 18 19 19 19 20 20 20 20 + 20 21 21 21 21 22 22 22 22 22 22 + 22 22 23 23 23 23 24 24 24 25 25 + 25 25 25 25 25 25 26 26 26 27 27 + 27 27 27 28 28 28 28 29 29 29 29 + 29 29 29 29 30 30 30 30 31 31 31 + 32 32 32 32 32 32 32 32 33 33 33 + 34 34 34 34 34 35 35 35 35 36 36 + 36 36 36 36 36 37 37 37 37 38 38 + 38 39 39 39 39 39 40 40 40 41 41 + 42 + 2 3 4 5 6 7 8 36 3 4 5 + 39 40 41 42 4 5 39 40 41 42 5 + 6 7 8 9 10 11 39 40 41 42 6 + 7 12 40 7 8 9 10 11 8 9 10 + 11 5 9 10 11 12 13 14 15 5 10 + 11 12 5 11 12 5 12 13 14 15 16 + 17 18 13 14 19 14 15 16 17 18 15 + 16 17 18 12 16 17 18 19 20 21 22 + 12 17 18 19 12 18 19 12 19 20 21 + 22 23 24 25 20 21 26 21 22 23 24 + 25 22 23 24 25 19 23 24 25 26 27 + 28 29 19 24 25 26 19 25 26 19 26 + 27 28 29 30 31 32 27 28 33 28 29 + 30 31 32 29 30 31 32 26 30 31 32 + 33 34 35 36 26 31 32 33 26 32 33 + 26 33 34 35 36 37 38 39 34 35 40 + 35 36 37 38 39 36 37 38 39 33 37 + 38 39 40 41 42 33 38 39 40 33 39 + 40 1 33 40 41 42 1 41 42 1 42 + 1 + ++
+
+ + diff --git a/doc/nwahtml/nwargos_extensions.html b/doc/nwahtml/nwargos_extensions.html new file mode 100644 index 0000000000..54f93704fa --- /dev/null +++ b/doc/nwahtml/nwargos_extensions.html @@ -0,0 +1,83 @@ + +
nwARGOS extensions
++
+File extensions +
+The following file extensions are used by nwARGOS and the setup +programs nwTOP, +nwRST and +nwSGM. +
+
| Extension | +File description | +
|---|---|
| coo | coordinate file | +
| inp | input file | +
| prp | property file | +
| rin | nwRST input file | +
| rou | nwRST output file | +
| rst | restart file | +
| seq | nwTOP sequence input file | +
| sco | solute coordinate file | +
| svl | solute velocity file | +
| top | topology file | +
| vel | velocity file | +
+
+Database extensions +
+The following file extensions are used by the setup programs +nwTOP, +nwRST and +nwSGM. +
+
| Extension | +File description | +
|---|---|
| att | atom type database | +
| frg | fragment database | +
| par | parameter database | +
| sgm | segment database | +
| slv | solvent restart file | +
nwARGOS file structure
++
+File names +
+File names used by nwARGOS need to have the form
+project_id.ext, with exception of the
+topology file, which should be named project.top, and the input
+file for NWChem, which should simply be project.
+Anything that refers to the definition of the chemical system can be used
+for project, as long as no periods or underlines are used.
+The identifier id can be anything that refers to the type of calculation
+to be performed for the system.
+The extensions ext
+identify the kind of information on the file, and are determined by the
+programs. Examples of extensions are top for the topology file,
+rst for the restart file and inp for the input file.
+
+This file naming convention allows for the creation of a single topology file +project.top for a chemical system with which a number of different +calculations, identified with different id. +
+
+
+Database names +
+A similar convention is used to identify databases used by the setup programs +nwTOP, +nwRST and +nwSGM. +Force field database names have the form +forcefield_level.ext, where forcefield stands for any of the +supported force fields. The source +of the data is identified by level, and can be +
+
| level | Description | Availability | +
|---|---|---|
| s | original published data | public | +
| x | additional published data | public | +
| u | user preferred data | private | +
| r | user defined run specific data | private | +
+Only the level s and x databases are publicly available. The user is +responsible for the private level u and r databases. +
+Other database files include the force field independent fragment libraries and +the solvation restart files. +
+
+ + diff --git a/doc/nwahtml/nwargos_forcefields.html b/doc/nwahtml/nwargos_forcefields.html new file mode 100644 index 0000000000..0824c7a02e --- /dev/null +++ b/doc/nwahtml/nwargos_forcefields.html @@ -0,0 +1,35 @@ + +
nwARGOS supported force fields
++
+Force fields supported by nwARGOS are +
+
| Keyword | Force field name | Current status | +
|---|---|---|
| amber | AMBER4.0 | available | +
| charmm | CHARMM | planned | +
| cvff | CVFF | planned | +
| gromos | GROMOS87 | planned | +
| oplsa | OPLS/AMBER3.0 | planned | +
| oplsg | OPLS/GROMOS87 | planned | +
+
+ + diff --git a/doc/nwahtml/nwargos_funct.html b/doc/nwahtml/nwargos_funct.html new file mode 100644 index 0000000000..29dac384d7 --- /dev/null +++ b/doc/nwahtml/nwargos_funct.html @@ -0,0 +1,9 @@ + +
nwARGOS molecular dynamics simulations functionality
++
+Functionality + + diff --git a/doc/nwahtml/nwargos_imple.html b/doc/nwahtml/nwargos_imple.html new file mode 100644 index 0000000000..262de8c04b --- /dev/null +++ b/doc/nwahtml/nwargos_imple.html @@ -0,0 +1,9 @@ + +
nwARGOS molecular dynamics simulations parallel implementation
++
+Parallel implementation + + diff --git a/doc/nwahtml/nwargos_input.html b/doc/nwahtml/nwargos_input.html new file mode 100644 index 0000000000..83eec75f4f --- /dev/null +++ b/doc/nwahtml/nwargos_input.html @@ -0,0 +1,325 @@ + +
nwARGOS input
++
+Input file format +
+The input file project_id.inp determines the type of calculation +to be performed. Details of the calculation are given in keyworded +format. +
+Input file keywords +
+Keywords need to be given exactly as given below. Numeric values are +in free format. Keywords recognized include +
+#
+Any card in the input file that starts with the number sign (#) is
+treated as a comment, and ignored.
+
+
+Any card in the input file that starts with a space is
+treated as a comment, and ignored.
+
+Title
+Three title cards (a) and one with date and time (2a10) are read.
+
+Task SP
+Identifies that a single point energy evaluation is to be done using
+parameters from set 1.
+This card cancels any previous Task cards in the input
+deck.
+
+Task SP set 2
+Identifies that a single point energy evaluation is to be done using
+parameters from set 2.
+This card cancels any previous Task cards in the input
+deck.
+
+Task SP set 3
+Identifies that a single point energy evaluation is to be done using
+parameters from set 3.
+This card cancels any previous Task cards in the input
+deck.
+
+Task MD
+Identifies that a molecular dynamics simulation is to be carried out using
+parameters from set 1.
+This card cancels any previous Task cards in the input
+deck.
+
+Task MD set 2
+Identifies that a molecular dynamics simulation is to be carried out using
+parameters from set 2.
+This card cancels any previous Task cards in the input
+deck.
+
+Task MD set 3
+Identifies that a molecular dynamics simulation is to be carried out using
+parameters from set 3.
+This card cancels any previous Task cards in the input
+deck.
+
+Task EM
+Identifies that an energy minimization is to be performed out using
+parameters from set 1.
+This card cancels any previous Task cards in the input
+deck.
+
+Task EM set 2
+Identifies that an energy minimization is to be performed out using
+parameters from set 2.
+This card cancels any previous Task cards in the input
+deck.
+
+Task EM set 3
+Identifies that an energy minimization is to be performed out using
+parameters from set 3.
+This card cancels any previous Task cards in the input
+deck.
+
+Task MCTI
+Identifies that a multiconfiguration thermodynamic integration
+calculation will be carried out.
+This card cancels any previous Task cards in the input
+deck.
+
+Start time rvalue
+This keywords sets the initial time for molecular dynamics simulations
+to rvalue. The default value is 0.000 ps.
+
+Time step rvalue
+This keywords sets the time-step for molecular dynamics simulations
+to rvalue. The default value is 0.001 ps.
+
+SD iterations ivalue
+This keywords sets the maximum number of steepest descent iterations
+for energy minimization calculations to ivalue.
+The default value is 100.
+
+SD initial step rvalue
+This keywords sets the initial step size for steepest descent
+energy minimization calculations to rvalue.
+The default value is 0.010 nm.
+
+CG iterations ivalue
+This keywords sets the maximum number of conjugate gradient iterations
+for energy minimization calculations to ivalue.
+The default value is 0.
+
+CG cycles ivalue
+This keywords sets the conjugate gradient refresh cycle
+for energy minimization calculations to ivalue.
+The default value is 0.
+
+MCTI windows total ivalue
+This keywords sets the total number of multiconfiguration
+thermodynamic integration steps for a free energy calculations
+to ivalue. The default value is 21.
+
+MCTI windows ivalue
+This keywords sets the number of multiconfiguration thermodynamic
+integration steps for a free energy calculation that will be done
+in this run to ivalue. The default value is equal to
+the total number of integration steps.
+
+MCTI separation shifted scaling delta rvalue
+This keywords sets the separation shifted scaling distance parameter
+delta to rvalue. The default, and recommended, value is
+0.075 nm^2.
+
+MCTI separation shifted scaling
+This keyword activates separation shifted scaling in MCTI free
+energy calculations. Per default separation shifted scaling is
+turned off.
+
+Print topology
+This keyword activates printing of the topology, for both solvent
+and solute. Per default the topology is not printed.
+
+Print topology solvent
+This keyword activates printing of the solvent topology.
+Per default the solvent topology is not printed.
+
+Print topology solute
+This keyword activates printing of the solute topology.
+Per default the solute topology is not printed.
+
+Print step
+This keyword activates printing of more detailed information
+at each printed time step. Per default only total system energies
+are printed.
+
+Print step energies
+This keyword activates printing of even more detailed energy information
+at each printed time step. Per default only total system energies
+are printed.
+
+Print timing analysis all nodes
+This keyword activates printing at the end of the run the timing
+analysis of all nodes. Per default only the timing analysis
+of node 0 is printed.
+
+Equilibration steps ivalue
+This keyword sets the number of equilibration steps in an MD run
+or in an MCTI window to ivalue. The default number
+of equilibration steps is 0.
+
+Data gathering steps ivalue
+This keyword sets the number of data gathering steps in an MD run
+or in an MCTI window to ivalue. The default number
+of data gathering steps is 100.
+
+Cutoff radius WW SR rvalue
+
+Cutoff radius WW LR rvalue
+
+Cutoff radius SW SR rvalue
+
+Cutoff radius WS SR rvalue
+
+Cutoff radius SW LR rvalue
+
+Cutoff radius WS LR rvalue
+
+Cutoff radius SS SR rvalue
+
+Cutoff radius SS LR rvalue
+
+Cutoff radius SR rvalue
+This keyword sets all short-range cutoff radii to rvalue.
+The default value is 0.9 nm.
+
+Cutoff radius LR rvalue
+This keyword sets all long-range cutoff radii to rvalue.
+The default value is 0.9 nm.
+
+Cutoff radius rvalue
+This keyword sets all cutoff radii to rvalue.
+The default value is 0.9 nm.
+
+SHAKE iterations W ivalue
+This keywrods sets the maximum number of solvent SHAKE iterations
+to ivalue. The default is 100.
+
+SHAKE iterations S ivalue
+This keywrods sets the maximum number of solute SHAKE iterations
+to ivalue. The default is 100.
+
+SHAKE iterations ivalue
+This keywrods sets the maximum number of SHAKE iterations
+to ivalue for both solvent and solute. The default is 100.
+
+SHAKE tolerance W rvalue
+This keyword sets the solvent SHAKE tolerance to rvalue.
+The default value is 0.001 nm.
+
+SHAKE tolerance S rvalue
+This keyword sets the solute SHAKE tolerance to rvalue.
+The default value is 0.001 nm.
+
+SHAKE tolerance rvalue
+This keyword sets the SHAKE tolerance to rvalue for both
+solvent and solute. The default value is 0.001 nm.
+
+Binary recording
+This keyword enables binary recording. Per default all
+recording files are ASCII formatted files.
+
+Frequency centering solute ivalue
+This keyword sets the frequency of centering the solute center
+of geometry. The default frequency is 0.
+
+Frequency update pairlists ivalue
+This keyword sets the frequency of updating the pairlists.
+The default frequency is 1.
+
+Frequency update LR forces ivalue
+This keyword sets the frequency of updating the long range forces.
+The default frequency is 1.
+
+Frequency recording output ivalue
+This keyword sets the frequency of recording selected information
+of a MD step, EM iteration or MCTI integration step to the output
+file to ivalue. The default frequency is 1.
+
+Frequency recording statistics ivalue
+This keyword sets the frequency of recording statistical information
+accumulated during MD and MCTI calculations to output to ivalue.
+The default frequency is 1.
+
+Frequency recording restart ivalue
+This keyword sets the frequency of recording the restart file to
+ivalue. The default value is 0.
+
+Frequency recording free energy ivalue
+This keyword sets the frequency of recording the free energy data to
+file to ivalue, during MCTI calculations. The default value
+is 1.
+
+Load balance box size
+This keyword specifies that loadbalancing is to be done based on
+resizing of sub-boxes. Per default no load balancing is done.
+
+Load balance box pairs
+This keyword specifies that loadbalancing is to be done based on
+redistribution of internode sub-box pairs. Per default no load
+balancing is done.
+
+Constant pressure rvalue
+This keyword specifies that the simulation is to be done for a
+constant pressure of rvalue Pa. Per default the simulation
+is at constant volume.
+
+Pressure relaxation time rvalue
+This keyword sets the pressure relation time to rvalue ps.
+The default value is 0.5 ps.
+
+Compressebility rvalue
+This keyword sets the compressebility of the molecular system
+to rvalue ps. The default value is 4.53 10^10.
+
+Constant temperature WS rvalue
+This keyword specifies that the simulation is to be done for a
+constant temperature of rvalue K, in which the scaling
+is done separately for solvent and solute. Per default the simulation
+is at constant energy.
+
+Constant temperature rvalue
+This keyword specifies that the simulation is to be done for a
+constant temperature of rvalue K, in which the scaling
+is done for the complete molecular system. Per default the simulation
+is at constant energy.
+
+Temperature relaxation time W rvalue
+This keyword sets the solvent temperature relation time to
+rvalue ps. The default value is 0.1 ps.
+
+Temperature relaxation time S rvalue
+This keyword sets the solute temperature relation time to
+rvalue ps. The default value is 0.1 ps.
+
+Temperature relaxation time rvalue
+This keyword sets the temperature relation time to
+rvalue ps for both solvent and solute.
+The default value is 0.1 ps.
+
+Velocity reassignment frequency WS ivalue
+The keyword sets the velocity reassignment frequency to ivalue
+for solvent and solute to separately obtain the reassigment
+temperature. The default value is 0.
+
+Velocity reassignment frequency ivalue
+The keyword sets the velocity reassignment frequency to ivalue
+for the molecular system to obtain the reassigment temperature.
+The default value is 0.
+
+Velocity reassignment temperature rvalue
+This keyword sets the velocity reassignment temperature. The default
+value is 298.15 K.
+
+
+ + diff --git a/doc/nwahtml/nwargos_intro.html b/doc/nwahtml/nwargos_intro.html new file mode 100644 index 0000000000..8c30a93ab4 --- /dev/null +++ b/doc/nwahtml/nwargos_intro.html @@ -0,0 +1,18 @@ + +
nwARGOS introduction
++
+nwArgos is the NWChem module for molecular dynamics +simulations of macromolecules and solutions. The code is a parallel +implementation of ARGOS, a vectorized molecular dynamics +package developed by T.P.Straatsma at the University of Houston. +
+The parallel implementation is based +on the spacial decomposition of the molecular system. This decomposition +makes the code especially efficient for large molecular systems. +
+
+ + diff --git a/doc/nwahtml/nwargos_nwRST.html b/doc/nwahtml/nwargos_nwRST.html new file mode 100644 index 0000000000..16a8987c8b --- /dev/null +++ b/doc/nwahtml/nwargos_nwRST.html @@ -0,0 +1,11 @@ + +
nwRST
++
+Restart generator +
+
+ + diff --git a/doc/nwahtml/nwargos_nwSGM.html b/doc/nwahtml/nwargos_nwSGM.html new file mode 100644 index 0000000000..e2bba39adc --- /dev/null +++ b/doc/nwahtml/nwargos_nwSGM.html @@ -0,0 +1,11 @@ + +
nwSGM
++
+Segment generator +
+
+ + diff --git a/doc/nwahtml/nwargos_nwTOP.html b/doc/nwahtml/nwargos_nwTOP.html new file mode 100644 index 0000000000..0757d952b8 --- /dev/null +++ b/doc/nwahtml/nwargos_nwTOP.html @@ -0,0 +1,42 @@ + +
Topology generator nwTOP
++
+The topology describes all static information +that describes a molecular system. This includes the connectivity, such +as bond-stretching, angle-bending and torsional interactions, as well as +non-bonded interactions, such as van der Waals and Coulombic interactions. +
+The topology of a molecular system is +generated by the topology generator nwTOP. The molecular system +is described in terms of segments taken out of a database of predefined +segments. Segments that are not available in one of the database files +can be generated bye a utility program +nwSGM. +
+The command line to run nwTOP is +
+nwtop project forcefield +
+where project is the name of a sequence on one of the +sequence databases or a local file project.seq, and +forcefield is the name of one of the +available force fields. +Force field parameters are taken from the parameter databases, +or from a local file project.par is present. The + format of the parameter +file is identical to the ARGOS parameter file +format. +The resulting topology file is project.top +
+The input for nwTOP is taken from a sequence database, or +given in a formatted sequence file project.seq. A sequence +file may be appended to a sequence database. The +format of a sequence +file is slightly different from the ARGOS sequence file +format. +
+ + diff --git a/doc/nwahtml/nwargos_nwinput.html b/doc/nwahtml/nwargos_nwinput.html new file mode 100644 index 0000000000..2dffafa82f --- /dev/null +++ b/doc/nwahtml/nwargos_nwinput.html @@ -0,0 +1,26 @@ + +
NWChem input
++
+NWChem input file format +
+The input file for NWChem determines the module that will +be executed. For the nwARGOS module this file should be named +project_id. To run a molecular dynamics job using nwARGOS, +this file only the memory card, start and task card are required. +
+
+An example of the input for NWChem is +
+
+title; nwARGOS
+memory noverify heap 1 mb stack 32 mb global 8 mb
+start nwarg
+task nwargos
+
+
+
+ + diff --git a/doc/nwahtml/nwargos_restart.html b/doc/nwahtml/nwargos_restart.html new file mode 100644 index 0000000000..7269b4746f --- /dev/null +++ b/doc/nwahtml/nwargos_restart.html @@ -0,0 +1,28 @@ + +
nwARGOS restart
++
+All dynamic information of a molecular system needed to start or
+restart a molecular simulation is provided in a restart file (rst).
+This file contains, among other things, atomic coordinates and velocities,
+accumulated properties and restraint information.
+
+The initial restart file is generated by a utility
+nwRST. This
+program reads coordinates from an external source and writes a
+restart file in the proper format for nwARGOS. The coordinates are
+read from a PDB file, or from the rst file generated by
+nwRST or nwARGOS. In addition,
+nwRST performs
+other operations, such as solvation, depending on information found
+in a restart input file (rin).
+
+
-
+
- Creating rin files +
- Creating rst files +
Sequence file format
++
| Card/Variable | +Format | +Description | +
|---|---|---|
| I/1 | A1 | $ needed as search character | +
| I/2 | A10 | Name of sequence | +
| II/1 | I5 | Segment number, or -1 to identify the +end of a molecule, -2 to identify the end of the solute part of +the system, -3 to identify the end of the sequence, or 0 to +identify the solvent |
+
| II/2 | A10 | Segment name for 0 or positive segment
+number + |
| II/3 | I5 | First link segment number | +
| II/4 | I3 | First link segment link atom | +
| II/5 | I5 | Second link segment number | +
| II/6 | I3 | Second link segment link atom | +
| II/7 | I5 | Third link segment number | +
| II/8 | I3 | Third link segment link atom | +
| II/9 | I5 | Fourth link segment number | +
| II/10 | I3 | Fourth link segment link atom | +
| II/11 | I5 | Fifth link segment number | +
| II/12 | I3 | Fifth link segment link atom | +
| II/13 | I5 | Sixth link segment number | +
| II/14 | I3 | Sixth link segment link atom | +
| II/15 | I5 | Seventh link segment number | +
| II/16 | I3 | Seventh link segment link atom | +
| II/17 | I5 | Eighth link segment number | +
| II/18 | I3 | Eighth link segment link atom | +
| II/19 | I5 | Ninth link segment number | +
| II/20 | I3 | Ninth link segment link atom | +
| II/21 | I5 | Tenth link segment number | +
| II/22 | I3 | Tenth link segment link atom | +
+Card I needs a $ as the first character, immediately followed
+by a 10 character identifying name for the system. These 11 characters
+are used as a search string by nwTOP. Any number of lines
+may preceed the first sequence card, for example to give a description
+of the sequence and its author.
+
+Card II identifies an individual segment. Any number of Cards II +can be specified. If solvent is specified +it needs to be the last specified segment. If not given, first links are +made automatically to the segment on the previous card, unless its +segment number is negative. If not given, second links are made +automatically to the segment on the next card, unless its segment +number is negative. +
+ + diff --git a/doc/nwahtml/nwargos_speedup_ksr2.gif b/doc/nwahtml/nwargos_speedup_ksr2.gif new file mode 100644 index 0000000000..04666bd67c Binary files /dev/null and b/doc/nwahtml/nwargos_speedup_ksr2.gif differ diff --git a/doc/nwahtml/nwargos_speedup_sp2.gif b/doc/nwahtml/nwargos_speedup_sp2.gif new file mode 100644 index 0000000000..0bc233cf10 Binary files /dev/null and b/doc/nwahtml/nwargos_speedup_sp2.gif differ diff --git a/doc/nwahtml/nwargos_topology.html b/doc/nwahtml/nwargos_topology.html new file mode 100644 index 0000000000..1869993bd8 --- /dev/null +++ b/doc/nwahtml/nwargos_topology.html @@ -0,0 +1,48 @@ + +
nwARGOS topology
++
+The static information about a molecular system that is needed for
+a molecular simulation is provided to the simulation module in a
+topology file (top).
+Items in this file include, among many other things,
+a list of atoms, their non-bonded parameters for van der Waals and
+electrostatic interactions, and a complete connectivity in terms
+of bonds, angles and dihedrals.
+
+In nwArgos, molecular systems are composed of solvent and
+solute, which are treated separately. Solvent, is a collection
+of identical molecules defined only once in the topology file. In the
+current implementation only one solvent can be defined. Everything
+else in the molecular system is solute. Solute is the collection of
+molecules in the system of which each atom is explicitly defined in
+the topology.
+
+Molecular systems are defined in terms of segments. Molecules
+can be defined in a single segment, or as a collection of segments.
+Typically, repetitive parts of a molecule are each defined as a single
+segment. Segment files (sgm) can be quite complicated to define
+and are, therefore, collected in a set of database libraries.
+The list of segments and their connectivity that make a molecular system
+is defined in a sequence file (seq).
+A utility nwTOP reads the sequence from this file, retrieves all
+needed segments from the available segment databases, and generates the
+topology file.
+
+Segments may not always be available in one of the existing databases.
+A utility nwSGM reads a rudimentary, force-field independent
+definition of a segment from a fragment file (frg), and
+constructs a template for a force-field dependent segment.
+Just like segments, fragments can be collected into a set of database files.
+
+
-
+
- Creating frg files +
- Creating sgm files +
- Creating seq files +
- Creating top files +
nwARGOS tutorial
++
+Performing a simulation with nwARGOS requires a minimum of the following +four files. Following the conventions of the +file structure, these are +
-
+
- project.top, describing the topology + of the molecular system, +
- project_id.rst, constaining the (re-)start + information, +
- project_id.inp, providing input details of + the simulation to nwARGOS, and +
- project_id, providing task and memory + information to NWChem. +
+Setting up a calculation is done in the following order +
-
+
- Create segment file project.sgm, using program + nwSGM, if needed +
- Create the topology file project.top, using program + nwTOP +
- Generate the restart file project_id.rst, using program + nwRST +
- Provide in the input file project_id.inp a stream of + keywords defining the simulation details +
- Provide in the NWChem input file project_id + the task and memory information +
+The actual simulation is carried out with +
+nwchem project_id +
+NWChem will read the file project_id, allocate the specified memory and +give control to the nwARGOS module. nwARGOS will strip the project_id +from the command line, and generate all needed filenames, such as project.top, +project_id.rst, and project_id.inp from it. + + diff --git a/doc/nwahtml/nwargos_xmpls.html b/doc/nwahtml/nwargos_xmpls.html new file mode 100644 index 0000000000..756eb106a0 --- /dev/null +++ b/doc/nwahtml/nwargos_xmpls.html @@ -0,0 +1,16 @@ + +
nwARGOS examples
++Example calculations available are +
+etoh: calculation of the absolute free +energy of hydration of ethanol. +
+crown: calculation of the free +energy difference between Na+ and K+ complexed in 18-crown-6. +
+
+ +