diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d22c85f09f56b0c09f23a706f870fc0b0ec7cac5
--- /dev/null
+++ b/doc/src/fix_filter_corotate.txt
@@ -0,0 +1,84 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix filter/corotate command :h3
+
+[Syntax:]
+
+fix ID group-ID filter/corotate keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+one or more constraint/value pairs are appended :l
+constraint = {b} or {a} or {t} or {m} :l
+ {b} values = one or more bond types
+ {a} values = one or more angle types
+ {t} values = one or more atom types
+ {m} value = one or more mass values :pre
+:ule
+
+[Examples:]
+
+timestep 8
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+fix cor all filter/corotate m 1.0 :pre
+
+fix cor all filter/corotate b 4 19 a 3 5 2 :pre
+
+[Description:]
+
+This fix implements a corotational filter for a mollified impulse method. In
+biomolecular simulations, it allows the usage of larger timesteps for
+long-range electrostatic interactions. For details, see "(Fath)"_#Fath2017.
+
+When using "run_style respa"_run_style.html for a biomolecular simulation with high-frequency covalent
+bonds, the outer time-step is restricted to below ~ 4fs due to resonance
+problems. This fix filters the outer stage of the respa and thus a larger
+(outer) time-step can be used. Since in large biomolecular simulations the
+computation of the long-range electrostatic contributions poses a major
+bottleneck, this can significantly accelerate the simulation.
+
+The filter computes a cluster decomposition of the molecular structure following
+the criteria indicated by the options a, b, t and m. This process is similar to
+the approach in "fix shake"_fix_shake.html, however, the clusters are not kept
+contrained. Instead, the position is slightly modified only for the computation
+of long-range forces. A good cluster decomposition constitutes in building
+clusters which contain the fastest covalent bonds inside clusters.
+
+If the clusters are chosen suitably, the "run_style respa"_run_style.html is stable for outer
+time-steps of at least 8fs.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about these fixes is written to "binary restart
+files"_restart.html. None of the "fix_modify"_fix_modify.html options
+are relevant to these fixes. No global or per-atom quantities are
+stored by these fixes for access by various "output
+commands"_Section_howto.html#howto_15. No parameter of these fixes
+can be used with the {start/stop} keywords of the "run"_run.html
+command. These fixes are not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+Currently, it does not support "molecule templates"_molecule.html.
+
+[Related commands:]
+
+
+[Default:] none
+
+:line
+
+:link(Fath2017)
+[(Fath)] Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
\ No newline at end of file
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index 7997f6f1d47ce442deea3d7231c80ccf41fd8d06..e8777d4113254c31dc7d0944cc9348a79b9c86d0 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -42,6 +42,7 @@ Fixes :h1
fix_eos_table_rx
fix_evaporate
fix_external
+ fix_filter_corotate
fix_flow_gauss
fix_freeze
fix_gcmc
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 3186865fb6a23e8800cc619c418f1ab626056b77..f942fdd344271cea0daba5945f4827f81749dd52 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -168,6 +168,7 @@ fix_eos_table.html
fix_eos_table_rx.html
fix_evaporate.html
fix_external.html
+fix_filter_corotate.html
fix_flow_gauss.html
fix_freeze.html
fix_gcmc.html
diff --git a/examples/USER/misc/filter-corotate/data.bpti b/examples/USER/misc/filter-corotate/data.bpti
new file mode 100644
index 0000000000000000000000000000000000000000..aee9184c037ee5c1911bf1d1cd912330ea4c5652
--- /dev/null
+++ b/examples/USER/misc/filter-corotate/data.bpti
@@ -0,0 +1,6587 @@
+Created by charmm2lammps v1.8.1 on Mi 27. Jan 08:43:59 CET 2016
+
+ 892 atoms
+ 906 bonds
+ 1626 angles
+ 2501 dihedrals
+ 137 impropers
+
+ 28 atom types
+ 51 bond types
+ 120 angle types
+ 232 dihedral types
+ 15 improper types
+
+ -10 50 xlo xhi
+ -10 50 ylo yhi
+ -30 30 zlo zhi
+
+Masses
+
+ 1 1.008 # H
+ 2 1.008 # HC
+ 3 1.008 # HA
+ 4 1.008 # HP
+ 5 1.008 # HB
+ 6 12.011 # C
+ 7 12.011 # CA
+ 8 12.011 # CT1
+ 9 12.011 # CT2
+ 10 12.011 # CT3
+ 11 12.011 # CP1
+ 12 12.011 # CP2
+ 13 12.011 # CP3
+ 14 12.011 # CC
+ 15 14.007 # N
+ 16 14.007 # NH1
+ 17 14.007 # NH2
+ 18 14.007 # NH3
+ 19 14.007 # NC2
+ 20 15.999 # O
+ 21 15.999 # OC
+ 22 15.999 # OH1
+ 23 32.06 # S
+ 24 32.06 # SM
+ 25 1.008 # HT
+ 26 15.9994 # OT
+ 27 35.45 # CLA
+ 28 22.98977 # SOD
+
+Pair Coeffs
+
+ 1 0.046 0.4000135 # 0.046 0.4000135 # H
+ 2 0.046 0.4000135 # 0.046 0.4000135 # HC
+ 3 0.022 2.351973 # 0.022 2.351973 # HA
+ 4 0.03 2.420037 # 0.03 2.420037 # HP
+ 5 0.022 2.351973 # 0.022 2.351973 # HB
+ 6 0.11 3.563595 # 0.11 3.563595 # C
+ 7 0.07 3.550053 # 0.07 3.550053 # CA
+ 8 0.02 4.053589 # 0.01 3.385415 # CT1
+ 9 0.055 3.875409 # 0.01 3.385415 # CT2
+ 10 0.08 3.670503 # 0.01 3.385415 # CT3
+ 11 0.02 4.053589 # 0.01 3.385415 # CP1
+ 12 0.055 3.875409 # 0.01 3.385415 # CP2
+ 13 0.055 3.875409 # 0.01 3.385415 # CP3
+ 14 0.07 3.563595 # 0.07 3.563595 # CC
+ 15 0.2 3.296325 # 0.0001 3.296325 # N
+ 16 0.2 3.296325 # 0.2 2.761786 # NH1
+ 17 0.2 3.296325 # 0.2 3.296325 # NH2
+ 18 0.2 3.296325 # 0.2 3.296325 # NH3
+ 19 0.2 3.296325 # 0.2 3.296325 # NC2
+ 20 0.12 3.029056 # 0.12 2.494516 # O
+ 21 0.12 3.029056 # 0.12 3.029056 # OC
+ 22 0.1521 3.153781 # 0.1521 3.153781 # OH1
+ 23 0.45 3.563595 # 0.45 3.563595 # S
+ 24 0.38 3.51905 # 0.38 3.51905 # SM
+ 25 0.046 0.4000135 # 0.046 0.4000135 # HT
+ 26 0.1521 3.150574 # 0.1521 3.150574 # OT
+ 27 0.15 4.04468 # 0.15 4.04468 # CLA
+ 28 0.0469 2.429926 # 0.0469 2.429926 # SOD
+
+Atoms
+
+ 1 1 18 -0.3 26.465 27.452 -2.49 # NH3
+ 2 1 2 0.33 25.974 27.9 -3.237 # HC
+ 3 1 2 0.33 27.052 26.729 -2.853 # HC
+ 4 1 2 0.33 27.017 28.122 -1.994 # HC
+ 5 1 8 0.21 25.497 26.862 -1.573 # CT1
+ 6 1 5 0.1 24.903 27.657 -1.139 # HB
+ 7 1 9 -0.18 24.583 25.804 -2.239 # CT2
+ 8 1 3 0.09 23.666 25.736 -1.606 # HA
+ 9 1 3 0.09 24.244 26.177 -3.231 # HA
+ 10 1 9 -0.18 25.091 24.375 -2.409 # CT2
+ 11 1 3 0.09 26.018 24.4 -3.023 # HA
+ 12 1 3 0.09 25.402 23.98 -1.414 # HA
+ 13 1 9 0.2 24.019 23.428 -2.996 # CT2
+ 14 1 3 0.09 24.459 22.415 -3.141 # HA
+ 15 1 3 0.09 23.136 23.341 -2.32 # HA
+ 16 1 19 -0.7 23.591 24.028 -4.287 # NC2
+ 17 1 2 0.44 22.696 24.486 -4.233 # HC
+ 18 1 6 0.64 24.299 23.972 -5.389 # C
+ 19 1 19 -0.8 25.432 23.261 -5.44 # NC2
+ 20 1 2 0.46 25.978 23.241 -6.266 # HC
+ 21 1 2 0.46 25.754 22.877 -4.572 # HC
+ 22 1 19 -0.8 23.721 24.373 -6.467 # NC2
+ 23 1 2 0.46 24.178 24.271 -7.339 # HC
+ 24 1 2 0.46 22.753 24.577 -6.407 # HC
+ 25 1 6 0.51 26.193 26.179 -0.437 # C
+ 26 1 20 -0.51 27.27 25.549 -0.624 # O
+ 27 2 15 -0.29 25.667 26.396 0.708 # N
+ 28 2 13 0 24.606 27.382 0.978 # CP3
+ 29 2 3 0.09 25.478 27.982 0.631 # HA
+ 30 2 3 0.09 23.663 27.767 0.526 # HA
+ 31 2 11 0.02 26.222 25.76 1.891 # CP1
+ 32 2 5 0.09 27.241 26.099 2.038 # HB
+ 33 2 12 -0.18 25.26 26.207 3.033 # CP2
+ 34 2 3 0.09 25.583 27.203 3.411 # HA
+ 35 2 3 0.09 25.237 25.491 3.879 # HA
+ 36 2 12 -0.18 24.512 27.428 2.493 # CP2
+ 37 2 3 0.09 24.117 28.082 3.295 # HA
+ 38 2 3 0.09 23.672 27.087 1.845 # HA
+ 39 2 6 0.51 26.207 24.242 1.83 # C
+ 40 2 20 -0.51 25.4 23.576 1.139 # O
+ 41 3 16 -0.47 27.17 23.634 2.462 # NH1
+ 42 3 1 0.31 27.898 24.092 2.965 # H
+ 43 3 8 0.07 27.284 22.163 2.498 # CT1
+ 44 3 5 0.09 27.355 21.833 1.468 # HB
+ 45 3 9 -0.28 28.425 21.747 3.461 # CT2
+ 46 3 3 0.09 28.41 22.407 4.351 # HA
+ 47 3 3 0.09 28.288 20.701 3.8 # HA
+ 48 3 14 0.62 29.791 21.886 2.787 # CC
+ 49 3 21 -0.76 29.875 22.104 1.543 # OC
+ 50 3 21 -0.76 30.806 21.501 3.431 # OC
+ 51 3 6 0.51 26.043 21.506 3.085 # C
+ 52 3 20 -0.51 25.752 20.35 2.705 # O
+ 53 4 16 -0.47 25.394 22.184 4.041 # NH1
+ 54 4 1 0.31 25.64 23.072 4.425 # H
+ 55 4 8 0.07 24.172 21.585 4.618 # CT1
+ 56 4 5 0.09 24.485 20.603 4.953 # HB
+ 57 4 9 -0.18 23.692 22.331 5.862 # CT2
+ 58 4 3 0.09 22.822 21.792 6.297 # HA
+ 59 4 3 0.09 24.483 22.359 6.642 # HA
+ 60 4 7 0 23.192 23.779 5.639 # CA
+ 61 4 7 -0.115 21.961 24.002 5.06 # CA
+ 62 4 4 0.115 21.356 23.161 4.748 # HP
+ 63 4 7 -0.115 21.497 25.281 4.869 # CA
+ 64 4 4 0.115 20.524 25.443 4.428 # HP
+ 65 4 7 -0.115 22.277 26.363 5.249 # CA
+ 66 4 4 0.115 21.941 27.378 5.091 # HP
+ 67 4 7 -0.115 23.951 24.841 6.05 # CA
+ 68 4 4 0.115 24.913 24.671 6.513 # HP
+ 69 4 7 -0.115 23.51 26.124 5.854 # CA
+ 70 4 4 0.115 24.122 26.958 6.169 # HP
+ 71 4 6 0.51 23.009 21.375 3.624 # C
+ 72 4 20 -0.51 22.082 20.603 3.921 # O
+ 73 5 16 -0.47 23.095 22.004 2.522 # NH1
+ 74 5 1 0.31 23.843 22.631 2.313 # H
+ 75 5 8 0.07 22.106 21.863 1.467 # CT1
+ 76 5 5 0.09 21.135 21.942 1.941 # HB
+ 77 5 9 -0.1 22.358 22.904 0.371 # CT2
+ 78 5 3 0.09 23.411 22.778 0.032 # HA
+ 79 5 3 0.09 21.722 22.681 -0.514 # HA
+ 80 5 24 -0.08 22.145 24.592 0.888 # SM
+ 81 5 6 0.51 22.192 20.518 0.83 # C
+ 82 5 20 -0.51 21.23 20.068 0.167 # O
+ 83 6 16 -0.47 23.326 19.826 1.008 # NH1
+ 84 6 1 0.31 24.141 20.141 1.49 # H
+ 85 6 8 0.07 23.436 18.46 0.459 # CT1
+ 86 6 5 0.09 22.788 18.447 -0.408 # HB
+ 87 6 9 -0.18 24.898 18.084 0.131 # CT2
+ 88 6 3 0.09 25.443 18.006 1.1 # HA
+ 89 6 3 0.09 24.918 17.065 -0.316 # HA
+ 90 6 8 -0.09 25.572 19.129 -0.776 # CT1
+ 91 6 3 0.09 25.596 20.032 -0.119 # HA
+ 92 6 10 -0.27 27.037 18.695 -1.116 # CT3
+ 93 6 3 0.09 27.509 19.424 -1.809 # HA
+ 94 6 3 0.09 27.654 18.642 -0.193 # HA
+ 95 6 3 0.09 27.048 17.697 -1.603 # HA
+ 96 6 10 -0.27 24.791 19.488 -2.049 # CT3
+ 97 6 3 0.09 25.338 20.259 -2.633 # HA
+ 98 6 3 0.09 24.65 18.606 -2.706 # HA
+ 99 6 3 0.09 23.79 19.895 -1.789 # HA
+ 100 6 6 0.51 22.958 17.365 1.407 # C
+ 101 6 20 -0.51 22.938 16.18 0.999 # O
+ 102 7 16 -0.47 22.545 17.716 2.628 # NH1
+ 103 7 1 0.31 22.529 18.626 3.032 # H
+ 104 7 8 0.07 22.039 16.646 3.528 # CT1
+ 105 7 5 0.09 22.645 15.758 3.402 # HB
+ 106 7 9 -0.18 21.764 17.217 4.92 # CT2
+ 107 7 3 0.09 20.871 17.88 4.853 # HA
+ 108 7 3 0.09 21.483 16.395 5.616 # HA
+ 109 7 9 -0.28 22.814 18.035 5.647 # CT2
+ 110 7 3 0.09 23.61 17.365 6.02 # HA
+ 111 7 3 0.09 23.261 18.794 4.975 # HA
+ 112 7 14 0.62 22.152 18.707 6.87 # CC
+ 113 7 21 -0.76 22.98 19.1 7.718 # OC
+ 114 7 21 -0.76 21.086 19.404 6.779 # OC
+ 115 7 6 0.51 20.616 16.285 3.113 # C
+ 116 7 20 -0.51 19.86 17.136 2.576 # O
+ 117 8 15 -0.29 20.254 15.031 3.334 # N
+ 118 8 13 0 21.107 14.009 3.934 # CP3
+ 119 8 3 0.09 21.793 13.937 3.059 # HA
+ 120 8 3 0.09 21.689 14.134 4.876 # HA
+ 121 8 11 0.02 18.892 14.554 3.034 # CP1
+ 122 8 5 0.09 18.556 14.845 2.045 # HB
+ 123 8 12 -0.18 18.91 13.045 3.274 # CP2
+ 124 8 3 0.09 19.279 12.536 2.355 # HA
+ 125 8 3 0.09 17.911 12.64 3.534 # HA
+ 126 8 12 -0.18 20.226 12.742 4.021 # CP2
+ 127 8 3 0.09 20.561 11.693 3.898 # HA
+ 128 8 3 0.09 20.092 12.964 5.105 # HA
+ 129 8 6 0.51 17.954 15.16 4.079 # C
+ 130 8 20 -0.51 18.443 15.606 5.146 # O
+ 131 9 15 -0.29 16.682 15.232 3.767 # N
+ 132 9 13 0 16.09 14.597 2.574 # CP3
+ 133 9 3 0.09 16.462 15.319 1.812 # HA
+ 134 9 3 0.09 16.367 13.555 2.292 # HA
+ 135 9 11 0.02 15.69 15.852 4.661 # CP1
+ 136 9 5 0.09 15.977 16.859 4.942 # HB
+ 137 9 12 -0.18 14.367 15.707 3.867 # CP2
+ 138 9 3 0.09 14.274 16.56 3.158 # HA
+ 139 9 3 0.09 13.473 15.685 4.523 # HA
+ 140 9 12 -0.18 14.571 14.716 2.71 # CP2
+ 141 9 3 0.09 13.847 14.861 1.884 # HA
+ 142 9 3 0.09 14.485 13.675 3.099 # HA
+ 143 9 6 0.51 15.55 15.006 5.916 # C
+ 144 9 20 -0.51 15.693 13.769 5.836 # O
+ 145 10 16 -0.47 15.365 15.63 7.042 # NH1
+ 146 10 1 0.31 15.251 16.618 7.126 # H
+ 147 10 8 0.07 15.31 14.908 8.298 # CT1
+ 148 10 5 0.09 15.352 13.849 8.072 # HB
+ 149 10 9 -0.18 16.532 15.383 9.122 # CT2
+ 150 10 3 0.09 17.465 15.08 8.598 # HA
+ 151 10 3 0.09 16.545 16.492 9.202 # HA
+ 152 10 7 0 16.608 14.781 10.525 # CA
+ 153 10 7 -0.115 17.132 13.535 10.707 # CA
+ 154 10 4 0.115 17.465 12.962 9.852 # HP
+ 155 10 7 -0.115 17.216 12.999 11.982 # CA
+ 156 10 4 0.115 17.594 11.999 12.134 # HP
+ 157 10 7 0.11 16.808 13.746 13.047 # CA
+ 158 10 22 -0.54 16.878 13.192 14.372 # OH1
+ 159 10 1 0.43 16.62 13.882 14.987 # H
+ 160 10 7 -0.115 16.155 15.523 11.588 # CA
+ 161 10 4 0.115 15.689 16.484 11.417 # HP
+ 162 10 7 -0.115 16.266 14.985 12.862 # CA
+ 163 10 4 0.115 15.902 15.542 13.712 # HP
+ 164 10 6 0.51 13.953 15.177 8.952 # C
+ 165 10 20 -0.51 13.699 16.32 9.382 # O
+ 166 11 16 -0.47 13.161 14.146 9.088 # NH1
+ 167 11 1 0.31 13.387 13.203 8.845 # H
+ 168 11 8 0.07 11.802 14.321 9.642 # CT1
+ 169 11 5 0.09 11.434 15.257 9.244 # HB
+ 170 11 8 0.14 10.963 13.105 9.273 # CT1
+ 171 11 3 0.09 11.604 12.213 9.477 # HA
+ 172 11 22 -0.66 10.706 13.192 7.854 # OH1
+ 173 11 1 0.43 10.166 12.423 7.643 # H
+ 174 11 10 -0.27 9.611 13.152 10.045 # CT3
+ 175 11 3 0.09 9.03 12.22 9.881 # HA
+ 176 11 3 0.09 9.791 13.254 11.136 # HA
+ 177 11 3 0.09 8.99 14.012 9.713 # HA
+ 178 11 6 0.51 11.855 14.484 11.146 # C
+ 179 11 20 -0.51 11.105 15.314 11.759 # O
+ 180 12 16 -0.47 12.789 13.76 11.726 # NH1
+ 181 12 1 0.31 13.385 13.097 11.274 # H
+ 182 12 9 -0.02 13.002 13.922 13.198 # CT2
+ 183 12 5 0.09 12.706 14.92 13.49 # HB
+ 184 12 5 0.09 14.026 13.674 13.441 # HB
+ 185 12 6 0.51 12.107 12.944 13.909 # C
+ 186 12 20 -0.51 11.333 12.212 13.239 # O
+ 187 13 15 -0.29 12.235 12.905 15.21 # N
+ 188 13 13 0 13.281 13.627 15.925 # CP3
+ 189 13 3 0.09 14.19 13.183 15.46 # HA
+ 190 13 3 0.09 13.319 14.739 15.871 # HA
+ 191 13 11 0.02 11.516 11.958 16.067 # CP1
+ 192 13 5 0.09 11.509 11.001 15.559 # HB
+ 193 13 12 -0.18 12.272 11.936 17.37 # CP2
+ 194 13 3 0.09 13.113 11.212 17.289 # HA
+ 195 13 3 0.09 11.634 11.652 18.231 # HA
+ 196 13 12 -0.18 13.164 13.172 17.399 # CP2
+ 197 13 3 0.09 14.034 13.061 18.075 # HA
+ 198 13 3 0.09 12.56 14.053 17.715 # HA
+ 199 13 6 0.51 10.094 12.319 16.468 # C
+ 200 13 20 -0.51 9.44 11.442 17.052 # O
+ 201 14 16 -0.47 9.629 13.519 16.214 # NH1
+ 202 14 1 0.31 10.174 14.196 15.723 # H
+ 203 14 8 0.07 8.29 13.98 16.616 # CT1
+ 204 14 5 0.09 8.005 13.387 17.477 # HB
+ 205 14 9 -0.1 8.279 15.441 16.967 # CT2
+ 206 14 3 0.09 8.747 15.988 16.118 # HA
+ 207 14 3 0.09 7.23 15.807 17.027 # HA
+ 208 14 24 -0.08 9.221 15.735 18.49 # SM
+ 209 14 6 0.51 7.268 13.72 15.515 # C
+ 210 14 20 -0.51 7.672 13.397 14.387 # O
+ 211 15 16 -0.47 6.027 13.68 15.869 # NH1
+ 212 15 1 0.31 5.692 13.952 16.77 # H
+ 213 15 8 0.07 5.005 13.22 14.945 # CT1
+ 214 15 5 0.09 5.517 12.984 14.02 # HB
+ 215 15 9 -0.18 4.31 11.998 15.592 # CT2
+ 216 15 3 0.09 3.83 12.354 16.533 # HA
+ 217 15 3 0.09 3.484 11.658 14.928 # HA
+ 218 15 9 -0.18 5.273 10.848 15.913 # CT2
+ 219 15 3 0.09 6.171 11.258 16.428 # HA
+ 220 15 3 0.09 4.776 10.146 16.621 # HA
+ 221 15 9 -0.18 5.781 10.034 14.702 # CT2
+ 222 15 3 0.09 4.91 9.522 14.232 # HA
+ 223 15 3 0.09 6.193 10.748 13.952 # HA
+ 224 15 9 0.21 6.855 9.016 15.126 # CT2
+ 225 15 3 0.05 7.711 9.533 15.615 # HA
+ 226 15 3 0.05 6.433 8.279 15.844 # HA
+ 227 15 18 -0.3 7.357 8.291 13.953 # NH3
+ 228 15 2 0.33 8.084 7.605 14.242 # HC
+ 229 15 2 0.33 6.571 7.789 13.493 # HC
+ 230 15 2 0.33 7.771 8.967 13.28 # HC
+ 231 15 6 0.51 3.964 14.283 14.63 # C
+ 232 15 20 -0.51 2.777 13.949 14.377 # O
+ 233 16 16 -0.47 4.325 15.549 14.618 # NH1
+ 234 16 1 0.31 5.223 15.809 14.972 # H
+ 235 16 8 0.07 3.513 16.64 14.122 # CT1
+ 236 16 5 0.09 2.471 16.527 14.397 # HB
+ 237 16 10 -0.27 3.984 17.995 14.67 # CT3
+ 238 16 3 0.09 3.892 18.002 15.777 # HA
+ 239 16 3 0.09 5.05 18.18 14.415 # HA
+ 240 16 3 0.09 3.373 18.833 14.27 # HA
+ 241 16 6 0.51 3.561 16.615 12.586 # C
+ 242 16 20 -0.51 4.27 15.752 12.023 # O
+ 243 17 16 -0.47 2.781 17.425 11.943 # NH1
+ 244 17 1 0.31 2.214 18.113 12.39 # H
+ 245 17 8 0.07 2.7 17.355 10.457 # CT1
+ 246 17 5 0.09 3.523 16.758 10.082 # HB
+ 247 17 9 -0.18 1.32 16.787 9.97 # CT2
+ 248 17 3 0.09 0.533 17.418 10.449 # HA
+ 249 17 3 0.09 1.217 16.948 8.874 # HA
+ 250 17 9 -0.18 1.186 15.339 10.395 # CT2
+ 251 17 3 0.09 2.055 14.771 9.997 # HA
+ 252 17 3 0.09 1.272 15.278 11.504 # HA
+ 253 17 9 0.2 -0.17 14.751 9.963 # CT2
+ 254 17 3 0.09 -0.324 14.936 8.875 # HA
+ 255 17 3 0.09 -0.217 13.653 10.148 # HA
+ 256 17 19 -0.7 -1.132 15.455 10.801 # NC2
+ 257 17 2 0.44 -1.421 16.339 10.415 # HC
+ 258 17 6 0.64 -1.531 14.913 11.939 # C
+ 259 17 19 -0.8 -1.172 13.658 12.165 # NC2
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+ 363 22 4 0.115 13.444 15.473 -1.328 # HP
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+ 416 26 1 0.31 19.924 15.993 -5.311 # H
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+ 418 26 5 0.09 21.229 15.827 -7.831 # HB
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+ 431 26 18 -0.3 21.821 11.437 -4.681 # NH3
+ 432 26 2 0.33 22.554 10.778 -4.349 # HC
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+ 434 26 2 0.33 21.007 11.4 -4.035 # HC
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+ 446 27 20 -0.51 16.909 19.707 -9.863 # O
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+ 448 28 1 0.31 18.739 19.17 -7.286 # H
+ 449 28 9 -0.02 18.626 21.036 -8.237 # CT2
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+ 454 29 16 -0.47 16.632 21.566 -6.97 # NH1
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+ 462 29 3 0.09 14.942 20.995 -8.635 # HA
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+ 464 29 3 0.09 12.814 19.736 -7.979 # HA
+ 465 29 3 0.09 13.841 20.192 -6.571 # HA
+ 466 29 3 0.09 12.351 21.135 -6.946 # HA
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+ 468 29 3 0.09 12.824 20.985 -10.037 # HA
+ 469 29 3 0.09 12.304 22.507 -9.244 # HA
+ 470 29 3 0.09 13.806 22.481 -10.235 # HA
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+ 473 30 16 -0.47 14.114 22.692 -4.605 # NH1
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+ 486 31 5 0.09 10.088 20.269 -3.238 # HB
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+ 491 31 3 0.09 10.781 18.811 -5.158 # HA
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+ 495 31 17 -0.62 12.461 16.246 -4.115 # NH2
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+ 500 32 16 -0.47 8.983 19.459 -1.072 # NH1
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+ 509 32 3 0.09 5.509 21.406 -0.082 # HA
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+ 546 34 3 0.09 4.161 16.315 5.335 # HA
+ 547 34 3 0.09 5.159 15.15 4.392 # HA
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+ 568 35 4 0.115 10.14 21.96 12.851 # HP
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+ 579 37 1 0.31 9.059 18.28 12.913 # H
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+ 610 39 6 0.64 15.268 17.831 21.574 # C
+ 611 39 19 -0.8 15.87 19.02 21.453 # NC2
+ 612 39 2 0.46 16.037 19.584 22.25 # HC
+ 613 39 2 0.46 16.255 19.233 20.552 # HC
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+ 615 39 2 0.46 14.972 17.885 23.565 # HC
+ 616 39 2 0.46 14.448 16.455 22.745 # HC
+ 617 39 6 0.51 15.644 18.605 14.798 # C
+ 618 39 20 -0.51 16.306 17.708 14.224 # O
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+ 624 40 3 0.09 13.814 21.285 12.486 # HA
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+ 626 40 3 0.09 15.151 21.54 11.312 # HA
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+ 628 40 20 -0.51 17.752 20.431 13.327 # O
+ 629 41 16 -0.47 17.282 19.622 11.271 # NH1
+ 630 41 1 0.31 16.626 19.18 10.661 # H
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+ 632 41 5 0.09 19.265 20.166 11.483 # HB
+ 633 41 9 -0.18 18.961 18.612 9.934 # CT2
+ 634 41 3 0.09 18.043 18.257 9.411 # HA
+ 635 41 3 0.09 19.696 18.865 9.138 # HA
+ 636 41 9 -0.18 19.486 17.515 10.843 # CT2
+ 637 41 3 0.09 20.273 17.938 11.508 # HA
+ 638 41 3 0.09 18.657 17.157 11.496 # HA
+ 639 41 9 -0.18 20.043 16.425 9.926 # CT2
+ 640 41 3 0.09 19.196 15.976 9.359 # HA
+ 641 41 3 0.09 20.722 16.908 9.185 # HA
+ 642 41 9 0.21 20.782 15.386 10.779 # CT2
+ 643 41 3 0.05 21.779 15.772 11.087 # HA
+ 644 41 3 0.05 20.199 15.147 11.696 # HA
+ 645 41 18 -0.3 20.985 14.137 10.021 # NH3
+ 646 41 2 0.33 21.488 13.441 10.609 # HC
+ 647 41 2 0.33 20.062 13.748 9.739 # HC
+ 648 41 2 0.33 21.546 14.338 9.169 # HC
+ 649 41 6 0.51 18.461 21.087 9.753 # C
+ 650 41 20 -0.51 17.371 21.708 9.79 # O
+ 651 42 16 -0.47 19.577 21.644 9.215 # NH1
+ 652 42 1 0.31 20.454 21.174 9.277 # H
+ 653 42 8 0.07 19.571 22.903 8.543 # CT1
+ 654 42 5 0.09 18.983 23.588 9.142 # HB
+ 655 42 9 -0.18 20.981 23.47 8.429 # CT2
+ 656 42 3 0.09 21.637 22.623 8.115 # HA
+ 657 42 3 0.09 21.019 24.21 7.6 # HA
+ 658 42 9 -0.18 21.461 24.047 9.786 # CT2
+ 659 42 3 0.09 20.586 24.486 10.313 # HA
+ 660 42 3 0.09 21.81 23.209 10.433 # HA
+ 661 42 9 0.2 22.614 25.047 9.608 # CT2
+ 662 42 3 0.09 23.254 25.04 10.52 # HA
+ 663 42 3 0.09 23.246 24.79 8.726 # HA
+ 664 42 19 -0.7 22.119 26.404 9.384 # NC2
+ 665 42 2 0.44 21.122 26.444 9.251 # HC
+ 666 42 6 0.64 22.948 27.426 9.37 # C
+ 667 42 19 -0.8 24.253 27.187 9.415 # NC2
+ 668 42 2 0.46 24.902 27.935 9.432 # HC
+ 669 42 2 0.46 24.525 26.235 9.568 # HC
+ 670 42 19 -0.8 22.472 28.634 9.297 # NC2
+ 671 42 2 0.46 23.088 29.402 9.198 # HC
+ 672 42 2 0.46 21.498 28.723 9.132 # HC
+ 673 42 6 0.51 18.898 22.847 7.144 # C
+ 674 42 20 -0.51 18.476 23.93 6.69 # O
+ 675 43 16 -0.47 18.87 21.715 6.474 # NH1
+ 676 43 1 0.31 19.251 20.832 6.747 # H
+ 677 43 8 0.07 18.21 21.713 5.169 # CT1
+ 678 43 5 0.09 18.387 22.688 4.728 # HB
+ 679 43 9 -0.18 18.745 20.506 4.379 # CT2
+ 680 43 3 0.09 19.856 20.534 4.425 # HA
+ 681 43 3 0.09 18.416 19.559 4.853 # HA
+ 682 43 14 0.55 18.295 20.592 2.909 # CC
+ 683 43 20 -0.55 17.721 21.629 2.499 # O
+ 684 43 17 -0.62 18.664 19.564 2.134 # NH2
+ 685 43 1 0.32 18.398 19.595 1.174 # H
+ 686 43 1 0.3 19.208 18.823 2.515 # H
+ 687 43 6 0.51 16.671 21.559 5.372 # C
+ 688 43 20 -0.51 16.068 20.466 5.197 # O
+ 689 44 16 -0.47 16.097 22.643 5.82 # NH1
+ 690 44 1 0.31 16.559 23.529 5.842 # H
+ 691 44 8 0.07 14.676 22.662 6.349 # CT1
+ 692 44 5 0.09 14.073 22.113 5.634 # HB
+ 693 44 9 -0.18 14.577 21.951 7.736 # CT2
+ 694 44 3 0.09 14.951 20.911 7.613 # HA
+ 695 44 3 0.09 15.232 22.455 8.475 # HA
+ 696 44 14 0.55 13.128 21.861 8.301 # CC
+ 697 44 20 -0.55 12.432 22.889 8.208 # O
+ 698 44 17 -0.62 12.975 21.035 9.288 # NH2
+ 699 44 1 0.32 12.059 20.942 9.669 # H
+ 700 44 1 0.3 13.749 20.503 9.617 # H
+ 701 44 6 0.51 14.157 24.102 6.384 # C
+ 702 44 20 -0.51 14.715 24.959 7.12 # O
+ 703 45 16 -0.47 13.324 24.438 5.381 # NH1
+ 704 45 1 0.31 12.933 23.766 4.754 # H
+ 705 45 8 0.07 12.918 25.817 5.12 # CT1
+ 706 45 5 0.09 13.316 26.41 5.934 # HB
+ 707 45 9 -0.18 13.372 26.373 3.741 # CT2
+ 708 45 3 0.09 12.898 25.774 2.933 # HA
+ 709 45 3 0.09 13.042 27.425 3.605 # HA
+ 710 45 7 0 14.913 26.192 3.701 # CA
+ 711 45 7 -0.115 15.492 25.002 3.268 # CA
+ 712 45 4 0.115 14.862 24.154 3.037 # HP
+ 713 45 7 -0.115 16.877 24.881 3.132 # CA
+ 714 45 4 0.115 17.305 23.964 2.753 # HP
+ 715 45 7 -0.115 17.659 25.957 3.487 # CA
+ 716 45 4 0.115 18.732 25.866 3.393 # HP
+ 717 45 7 -0.115 15.705 27.252 4.053 # CA
+ 718 45 4 0.115 15.256 28.16 4.43 # HP
+ 719 45 7 -0.115 17.109 27.126 3.941 # CA
+ 720 45 4 0.115 17.748 27.954 4.216 # HP
+ 721 45 6 0.51 11.388 25.961 5.164 # C
+ 722 45 20 -0.51 10.669 24.966 4.915 # O
+ 723 46 16 -0.47 10.949 27.147 5.46 # NH1
+ 724 46 1 0.31 11.491 27.96 5.669 # H
+ 725 46 8 0.07 9.48 27.343 5.498 # CT1
+ 726 46 5 0.09 9.062 26.397 5.819 # HB
+ 727 46 9 -0.18 9.045 28.475 6.433 # CT2
+ 728 46 3 0.09 9.681 29.359 6.196 # HA
+ 729 46 3 0.09 8 28.767 6.186 # HA
+ 730 46 9 -0.18 9.258 27.946 7.875 # CT2
+ 731 46 3 0.09 8.507 27.151 8.086 # HA
+ 732 46 3 0.09 10.266 27.477 7.944 # HA
+ 733 46 9 -0.18 9.119 29.052 8.948 # CT2
+ 734 46 3 0.09 9.387 30.028 8.484 # HA
+ 735 46 3 0.09 8.048 29.11 9.25 # HA
+ 736 46 9 0.21 10.025 28.736 10.167 # CT2
+ 737 46 3 0.05 9.787 27.73 10.579 # HA
+ 738 46 3 0.05 11.097 28.751 9.871 # HA
+ 739 46 18 -0.3 9.826 29.728 11.231 # NH3
+ 740 46 2 0.33 10.437 29.506 12.044 # HC
+ 741 46 2 0.33 10.061 30.675 10.871 # HC
+ 742 46 2 0.33 8.831 29.715 11.534 # HC
+ 743 46 6 0.51 8.875 27.67 4.157 # C
+ 744 46 20 -0.51 7.634 27.623 4.057 # O
+ 745 47 16 -0.47 9.687 27.909 3.152 # NH1
+ 746 47 1 0.31 10.686 27.935 3.181 # H
+ 747 47 8 0.07 9.124 28.168 1.84 # CT1
+ 748 47 5 0.09 8.243 27.546 1.75 # HB
+ 749 47 9 0.05 8.778 29.648 1.642 # CT2
+ 750 47 3 0.09 8.157 29.738 0.722 # HA
+ 751 47 3 0.09 8.16 30.019 2.491 # HA
+ 752 47 22 -0.66 10 30.391 1.484 # OH1
+ 753 47 1 0.43 9.76 31.262 1.143 # H
+ 754 47 6 0.51 10.108 27.719 0.765 # C
+ 755 47 20 -0.51 11.332 27.66 1.047 # O
+ 756 48 16 -0.47 9.604 27.471 -0.422 # NH1
+ 757 48 1 0.31 8.635 27.471 -0.667 # H
+ 758 48 8 0.07 10.526 27.161 -1.512 # CT1
+ 759 48 5 0.09 11.187 26.352 -1.222 # HB
+ 760 48 10 -0.27 9.782 26.679 -2.783 # CT3
+ 761 48 3 0.09 9.168 25.786 -2.539 # HA
+ 762 48 3 0.09 9.101 27.468 -3.17 # HA
+ 763 48 3 0.09 10.492 26.397 -3.591 # HA
+ 764 48 6 0.51 11.423 28.346 -1.863 # C
+ 765 48 20 -0.51 12.634 28.115 -2.136 # O
+ 766 49 16 -0.47 10.966 29.57 -1.682 # NH1
+ 767 49 1 0.31 10.059 29.766 -1.319 # H
+ 768 49 8 0.07 11.751 30.764 -1.998 # CT1
+ 769 49 5 0.09 12.176 30.626 -2.985 # HB
+ 770 49 9 -0.18 10.871 32.022 -2.024 # CT2
+ 771 49 3 0.09 10.303 32.068 -1.066 # HA
+ 772 49 3 0.09 11.513 32.931 -2.042 # HA
+ 773 49 9 -0.28 9.868 32.069 -3.2 # CT2
+ 774 49 3 0.09 9.638 33.122 -3.447 # HA
+ 775 49 3 0.09 10.283 31.566 -4.096 # HA
+ 776 49 14 0.62 8.525 31.417 -2.847 # CC
+ 777 49 21 -0.76 7.573 31.562 -3.638 # OC
+ 778 49 21 -0.76 8.368 30.637 -1.865 # OC
+ 779 49 6 0.51 12.9 30.964 -1.04 # C
+ 780 49 20 -0.51 14.032 31.282 -1.463 # O
+ 781 50 16 -0.47 12.658 30.686 0.225 # NH1
+ 782 50 1 0.31 11.809 30.418 0.673 # H
+ 783 50 8 0.07 13.804 30.775 1.163 # CT1
+ 784 50 5 0.09 14.307 31.711 0.946 # HB
+ 785 50 9 -0.28 13.347 30.5 2.601 # CT2
+ 786 50 3 0.09 12.535 29.745 2.588 # HA
+ 787 50 3 0.09 14.184 30.101 3.207 # HA
+ 788 50 14 0.62 12.813 31.776 3.236 # CC
+ 789 50 21 -0.76 12.716 32.875 2.613 # OC
+ 790 50 21 -0.76 12.096 31.598 4.247 # OC
+ 791 50 6 0.51 14.824 29.667 0.941 # C
+ 792 50 20 -0.51 16.058 29.904 1.049 # O
+ 793 51 16 -0.47 14.305 28.478 0.644 # NH1
+ 794 51 1 0.31 13.321 28.322 0.585 # H
+ 795 51 8 0.07 15.128 27.301 0.379 # CT1
+ 796 51 5 0.09 15.783 27.179 1.234 # HB
+ 797 51 9 -0.1 14.238 26.045 0.259 # CT2
+ 798 51 3 0.09 13.759 25.884 1.251 # HA
+ 799 51 3 0.09 13.407 26.238 -0.455 # HA
+ 800 51 24 -0.08 15.047 24.53 -0.176 # SM
+ 801 51 6 0.51 16.006 27.523 -0.852 # C
+ 802 51 20 -0.51 17.248 27.267 -0.809 # O
+ 803 52 16 -0.47 15.384 28.062 -1.87 # NH1
+ 804 52 1 0.31 14.429 28.337 -1.962 # H
+ 805 52 8 0.07 16.192 28.302 -3.048 # CT1
+ 806 52 5 0.09 16.774 27.404 -3.216 # HB
+ 807 52 9 -0.18 15.267 28.571 -4.266 # CT2
+ 808 52 3 0.09 14.495 29.303 -3.931 # HA
+ 809 52 3 0.09 15.85 29.077 -5.068 # HA
+ 810 52 9 -0.14 14.634 27.261 -4.708 # CT2
+ 811 52 3 0.09 14.045 26.817 -3.878 # HA
+ 812 52 3 0.09 13.936 27.45 -5.552 # HA
+ 813 52 23 -0.09 15.759 25.962 -5.253 # S
+ 814 52 10 -0.22 16.307 26.625 -6.805 # CT3
+ 815 52 3 0.09 17.02 25.933 -7.302 # HA
+ 816 52 3 0.09 15.45 26.787 -7.494 # HA
+ 817 52 3 0.09 16.821 27.6 -6.664 # HA
+ 818 52 6 0.51 17.171 29.453 -2.841 # C
+ 819 52 20 -0.51 18.246 29.474 -3.49 # O
+ 820 53 16 -0.47 16.776 30.47 -2.099 # NH1
+ 821 53 1 0.31 15.877 30.5 -1.669 # H
+ 822 53 8 0.07 17.652 31.617 -1.869 # CT1
+ 823 53 5 0.09 17.981 32.02 -2.819 # HB
+ 824 53 9 -0.18 16.934 32.595 -0.93 # CT2
+ 825 53 3 0.09 16.01 32.924 -1.464 # HA
+ 826 53 3 0.09 16.587 32.053 -0.023 # HA
+ 827 53 9 -0.18 17.721 33.839 -0.54 # CT2
+ 828 53 3 0.09 18.362 33.592 0.335 # HA
+ 829 53 3 0.09 18.426 34.095 -1.364 # HA
+ 830 53 9 0.2 16.741 35.039 -0.291 # CT2
+ 831 53 3 0.09 17.25 35.81 0.332 # HA
+ 832 53 3 0.09 16.419 35.509 -1.249 # HA
+ 833 53 19 -0.7 15.472 34.668 0.404 # NC2
+ 834 53 2 0.44 15.624 34.222 1.293 # HC
+ 835 53 6 0.64 14.256 34.89 -0.074 # C
+ 836 53 19 -0.8 13.983 35.465 -1.233 # NC2
+ 837 53 2 0.46 13.045 35.619 -1.511 # HC
+ 838 53 2 0.46 14.762 35.849 -1.733 # HC
+ 839 53 19 -0.8 13.26 34.543 0.66 # NC2
+ 840 53 2 0.46 12.338 34.611 0.305 # HC
+ 841 53 2 0.46 13.466 34.023 1.479 # HC
+ 842 53 6 0.51 18.91 31.126 -1.141 # C
+ 843 53 20 -0.51 20.05 31.47 -1.556 # O
+ 844 54 16 -0.47 18.727 30.199 -0.237 # NH1
+ 845 54 1 0.31 17.86 29.777 0.026 # H
+ 846 54 8 0.07 19.89 29.693 0.496 # CT1
+ 847 54 5 0.09 20.559 30.536 0.601 # HB
+ 848 54 8 0.14 19.416 29.106 1.823 # CT1
+ 849 54 3 0.09 18.729 28.264 1.562 # HA
+ 850 54 22 -0.66 18.644 30.132 2.537 # OH1
+ 851 54 1 0.43 18.378 29.722 3.367 # H
+ 852 54 10 -0.27 20.616 28.506 2.662 # CT3
+ 853 54 3 0.09 20.243 27.984 3.568 # HA
+ 854 54 3 0.09 21.184 27.771 2.054 # HA
+ 855 54 3 0.09 21.317 29.305 2.986 # HA
+ 856 54 6 0.51 20.637 28.649 -0.297 # C
+ 857 54 20 -0.51 21.871 28.686 -0.287 # O
+ 858 55 16 -0.47 19.988 27.747 -0.961 # NH1
+ 859 55 1 0.31 19.012 27.789 -1.167 # H
+ 860 55 8 0.07 20.669 26.564 -1.471 # CT1
+ 861 55 5 0.09 21.675 26.615 -1.071 # HB
+ 862 55 9 -0.1 19.956 25.26 -1.056 # CT2
+ 863 55 3 0.09 18.877 25.382 -1.301 # HA
+ 864 55 3 0.09 20.319 24.416 -1.682 # HA
+ 865 55 24 -0.08 20.128 24.914 0.713 # SM
+ 866 55 6 0.51 20.773 26.534 -2.963 # C
+ 867 55 20 -0.51 21.341 25.553 -3.498 # O
+ 868 56 16 -0.47 20.132 27.442 -3.608 # NH1
+ 869 56 1 0.31 19.714 28.266 -3.227 # H
+ 870 56 9 -0.02 19.987 27.268 -5.071 # CT2
+ 871 56 5 0.09 19.223 27.965 -5.388 # HB
+ 872 56 5 0.09 19.737 26.229 -5.237 # HB
+ 873 56 6 0.51 21.257 27.575 -5.849 # C
+ 874 56 20 -0.51 21.386 27.129 -7.018 # O
+ 875 57 16 -0.47 22.225 28.05 -5.113 # NH1
+ 876 57 1 0.31 22.009 28.394 -4.2 # H
+ 877 57 9 -0.02 23.639 28.131 -5.505 # CT2
+ 878 57 5 0.09 23.862 27.28 -6.134 # HB
+ 879 57 5 0.09 24.238 28.189 -4.606 # HB
+ 880 57 6 0.51 23.887 29.393 -6.316 # C
+ 881 57 20 -0.51 22.949 30.065 -6.822 # O
+ 882 58 16 -0.47 25.146 29.681 -6.493 # NH1
+ 883 58 1 0.31 25.863 29.104 -6.103 # H
+ 884 58 8 0.07 25.617 30.84 -7.256 # CT1
+ 885 58 5 0.09 25.151 31.747 -6.888 # HB
+ 886 58 10 -0.27 27.16 30.98 -7.146 # CT3
+ 887 58 3 0.09 27.448 31.108 -6.081 # HA
+ 888 58 3 0.09 27.672 30.071 -7.531 # HA
+ 889 58 3 0.09 27.532 31.862 -7.71 # HA
+ 890 58 14 0.34 25.248 30.735 -8.729 # CC
+ 891 58 21 -0.67 24.75 29.881 -8.88 # OC
+ 892 58 21 -0.67 25.588 31.544 -9.208 # OC
+
+Bond Coeffs
+
+ 1 250 1.49 # C CP1
+ 2 250 1.49 # C CT1
+ 3 250 1.49 # C CT2
+ 4 260 1.3 # C N
+ 5 463 1.365 # C NC2
+ 6 370 1.345 # C NH1
+ 7 620 1.23 # C O
+ 8 305 1.375 # CA CA
+ 9 230 1.49 # CA CT2
+ 10 340 1.08 # CA HP
+ 11 334.3 1.411 # CA OH1
+ 12 200 1.522 # CC CT1
+ 13 200 1.522 # CC CT2
+ 14 430 1.36 # CC NH2
+ 15 650 1.23 # CC O
+ 16 525 1.26 # CC OC
+ 17 222.5 1.527 # CP1 CP2
+ 18 330 1.08 # CP1 HB
+ 19 320 1.434 # CP1 N
+ 20 222.5 1.537 # CP2 CP2
+ 21 222.5 1.537 # CP2 CP3
+ 22 309 1.111 # CP2 HA
+ 23 309 1.111 # CP3 HA
+ 24 320 1.455 # CP3 N
+ 25 222.5 1.5 # CT1 CT1
+ 26 222.5 1.538 # CT1 CT2
+ 27 222.5 1.538 # CT1 CT3
+ 28 309 1.111 # CT1 HA
+ 29 330 1.08 # CT1 HB
+ 30 320 1.43 # CT1 NH1
+ 31 200 1.48 # CT1 NH3
+ 32 428 1.42 # CT1 OH1
+ 33 222.5 1.53 # CT2 CT2
+ 34 222.5 1.528 # CT2 CT3
+ 35 309 1.111 # CT2 HA
+ 36 330 1.08 # CT2 HB
+ 37 261 1.49 # CT2 NC2
+ 38 320 1.43 # CT2 NH1
+ 39 200 1.48 # CT2 NH3
+ 40 428 1.42 # CT2 OH1
+ 41 198 1.818 # CT2 S
+ 42 214 1.816 # CT2 SM
+ 43 322 1.111 # CT3 HA
+ 44 240 1.816 # CT3 S
+ 45 440 0.997 # H NH1
+ 46 480 1 # H NH2
+ 47 545 0.96 # H OH1
+ 48 455 1 # HC NC2
+ 49 403 1.04 # HC NH3
+ 50 450 0.9572 # HT OT
+ 51 173 2.029 # SM SM
+
+Bonds
+
+ 1 31 1 5 # CT1 NH3
+ 2 49 2 1 # HC NH3
+ 3 49 3 1 # HC NH3
+ 4 49 4 1 # HC NH3
+ 5 29 5 6 # CT1 HB
+ 6 26 7 5 # CT1 CT2
+ 7 35 7 8 # CT2 HA
+ 8 35 7 9 # CT2 HA
+ 9 33 10 7 # CT2 CT2
+ 10 35 10 11 # CT2 HA
+ 11 35 10 12 # CT2 HA
+ 12 33 13 10 # CT2 CT2
+ 13 35 13 14 # CT2 HA
+ 14 35 13 15 # CT2 HA
+ 15 37 16 13 # CT2 NC2
+ 16 48 16 17 # HC NC2
+ 17 5 18 16 # C NC2
+ 18 5 18 19 # C NC2
+ 19 48 19 20 # HC NC2
+ 20 48 19 21 # HC NC2
+ 21 5 22 18 # C NC2
+ 22 48 22 23 # HC NC2
+ 23 48 22 24 # HC NC2
+ 24 2 25 5 # C CT1
+ 25 4 25 27 # C N
+ 26 7 26 25 # C O
+ 27 19 27 31 # CP1 N
+ 28 24 27 28 # CP3 N
+ 29 23 29 28 # CP3 HA
+ 30 23 30 28 # CP3 HA
+ 31 17 31 33 # CP1 CP2
+ 32 18 32 31 # CP1 HB
+ 33 20 33 36 # CP2 CP2
+ 34 22 34 33 # CP2 HA
+ 35 22 35 33 # CP2 HA
+ 36 21 36 28 # CP2 CP3
+ 37 22 37 36 # CP2 HA
+ 38 22 38 36 # CP2 HA
+ 39 1 39 31 # C CP1
+ 40 6 39 41 # C NH1
+ 41 7 40 39 # C O
+ 42 45 41 42 # H NH1
+ 43 30 41 43 # CT1 NH1
+ 44 29 43 44 # CT1 HB
+ 45 26 45 43 # CT1 CT2
+ 46 35 45 46 # CT2 HA
+ 47 35 45 47 # CT2 HA
+ 48 13 48 45 # CC CT2
+ 49 16 48 49 # CC OC
+ 50 16 50 48 # CC OC
+ 51 2 51 43 # C CT1
+ 52 6 51 53 # C NH1
+ 53 7 52 51 # C O
+ 54 45 53 54 # H NH1
+ 55 30 53 55 # CT1 NH1
+ 56 29 55 56 # CT1 HB
+ 57 26 57 55 # CT1 CT2
+ 58 35 57 58 # CT2 HA
+ 59 35 57 59 # CT2 HA
+ 60 9 60 57 # CA CT2
+ 61 10 61 62 # CA HP
+ 62 8 61 60 # CA CA
+ 63 8 63 61 # CA CA
+ 64 10 63 64 # CA HP
+ 65 8 65 69 # CA CA
+ 66 8 65 63 # CA CA
+ 67 10 65 66 # CA HP
+ 68 8 67 60 # CA CA
+ 69 10 67 68 # CA HP
+ 70 8 69 67 # CA CA
+ 71 10 69 70 # CA HP
+ 72 2 71 55 # C CT1
+ 73 6 71 73 # C NH1
+ 74 7 72 71 # C O
+ 75 45 73 74 # H NH1
+ 76 30 73 75 # CT1 NH1
+ 77 29 75 76 # CT1 HB
+ 78 26 77 75 # CT1 CT2
+ 79 35 77 78 # CT2 HA
+ 80 35 77 79 # CT2 HA
+ 81 51 80 865 # SM SM
+ 82 42 80 77 # CT2 SM
+ 83 2 81 75 # C CT1
+ 84 6 81 83 # C NH1
+ 85 7 82 81 # C O
+ 86 45 83 84 # H NH1
+ 87 30 83 85 # CT1 NH1
+ 88 29 85 86 # CT1 HB
+ 89 26 87 85 # CT1 CT2
+ 90 35 87 88 # CT2 HA
+ 91 35 87 89 # CT2 HA
+ 92 26 90 87 # CT1 CT2
+ 93 28 90 91 # CT1 HA
+ 94 27 92 90 # CT1 CT3
+ 95 43 92 93 # CT3 HA
+ 96 43 92 94 # CT3 HA
+ 97 43 92 95 # CT3 HA
+ 98 27 96 90 # CT1 CT3
+ 99 43 96 97 # CT3 HA
+ 100 43 96 98 # CT3 HA
+ 101 43 96 99 # CT3 HA
+ 102 2 100 85 # C CT1
+ 103 6 100 102 # C NH1
+ 104 7 101 100 # C O
+ 105 45 102 103 # H NH1
+ 106 30 102 104 # CT1 NH1
+ 107 29 104 105 # CT1 HB
+ 108 26 106 104 # CT1 CT2
+ 109 35 106 107 # CT2 HA
+ 110 35 106 108 # CT2 HA
+ 111 33 109 106 # CT2 CT2
+ 112 35 109 110 # CT2 HA
+ 113 35 109 111 # CT2 HA
+ 114 13 112 109 # CC CT2
+ 115 16 112 113 # CC OC
+ 116 16 114 112 # CC OC
+ 117 2 115 104 # C CT1
+ 118 4 115 117 # C N
+ 119 7 116 115 # C O
+ 120 19 117 121 # CP1 N
+ 121 24 117 118 # CP3 N
+ 122 23 119 118 # CP3 HA
+ 123 23 120 118 # CP3 HA
+ 124 17 121 123 # CP1 CP2
+ 125 18 122 121 # CP1 HB
+ 126 20 123 126 # CP2 CP2
+ 127 22 124 123 # CP2 HA
+ 128 22 125 123 # CP2 HA
+ 129 21 126 118 # CP2 CP3
+ 130 22 127 126 # CP2 HA
+ 131 22 128 126 # CP2 HA
+ 132 1 129 121 # C CP1
+ 133 4 129 131 # C N
+ 134 7 130 129 # C O
+ 135 19 131 135 # CP1 N
+ 136 24 131 132 # CP3 N
+ 137 23 133 132 # CP3 HA
+ 138 23 134 132 # CP3 HA
+ 139 17 135 137 # CP1 CP2
+ 140 18 136 135 # CP1 HB
+ 141 20 137 140 # CP2 CP2
+ 142 22 138 137 # CP2 HA
+ 143 22 139 137 # CP2 HA
+ 144 21 140 132 # CP2 CP3
+ 145 22 141 140 # CP2 HA
+ 146 22 142 140 # CP2 HA
+ 147 1 143 135 # C CP1
+ 148 6 143 145 # C NH1
+ 149 7 144 143 # C O
+ 150 45 145 146 # H NH1
+ 151 30 145 147 # CT1 NH1
+ 152 29 147 148 # CT1 HB
+ 153 26 149 147 # CT1 CT2
+ 154 35 149 150 # CT2 HA
+ 155 35 149 151 # CT2 HA
+ 156 9 152 149 # CA CT2
+ 157 10 153 154 # CA HP
+ 158 8 153 152 # CA CA
+ 159 8 155 153 # CA CA
+ 160 10 155 156 # CA HP
+ 161 8 155 157 # CA CA
+ 162 8 157 162 # CA CA
+ 163 11 158 157 # CA OH1
+ 164 47 158 159 # H OH1
+ 165 8 160 152 # CA CA
+ 166 10 160 161 # CA HP
+ 167 10 162 163 # CA HP
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+ 853 5 839 835 # C NC2
+ 854 48 839 840 # HC NC2
+ 855 48 839 841 # HC NC2
+ 856 2 842 822 # C CT1
+ 857 6 842 844 # C NH1
+ 858 7 843 842 # C O
+ 859 45 844 845 # H NH1
+ 860 30 844 846 # CT1 NH1
+ 861 29 846 847 # CT1 HB
+ 862 25 848 846 # CT1 CT1
+ 863 28 848 849 # CT1 HA
+ 864 32 850 848 # CT1 OH1
+ 865 47 850 851 # H OH1
+ 866 27 852 848 # CT1 CT3
+ 867 43 852 853 # CT3 HA
+ 868 43 852 854 # CT3 HA
+ 869 43 852 855 # CT3 HA
+ 870 2 856 846 # C CT1
+ 871 6 856 858 # C NH1
+ 872 7 857 856 # C O
+ 873 45 858 859 # H NH1
+ 874 30 858 860 # CT1 NH1
+ 875 29 860 861 # CT1 HB
+ 876 26 862 860 # CT1 CT2
+ 877 35 862 863 # CT2 HA
+ 878 35 862 864 # CT2 HA
+ 879 42 865 862 # CT2 SM
+ 880 2 866 860 # C CT1
+ 881 6 866 868 # C NH1
+ 882 7 867 866 # C O
+ 883 45 868 869 # H NH1
+ 884 38 868 870 # CT2 NH1
+ 885 36 870 871 # CT2 HB
+ 886 36 870 872 # CT2 HB
+ 887 3 873 870 # C CT2
+ 888 6 873 875 # C NH1
+ 889 7 874 873 # C O
+ 890 45 875 876 # H NH1
+ 891 38 875 877 # CT2 NH1
+ 892 36 877 878 # CT2 HB
+ 893 36 877 879 # CT2 HB
+ 894 3 880 877 # C CT2
+ 895 6 880 882 # C NH1
+ 896 7 881 880 # C O
+ 897 45 882 883 # H NH1
+ 898 30 882 884 # CT1 NH1
+ 899 29 884 885 # CT1 HB
+ 900 27 886 884 # CT1 CT3
+ 901 43 886 887 # CT3 HA
+ 902 43 886 888 # CT3 HA
+ 903 43 886 889 # CT3 HA
+ 904 16 890 892 # CC OC
+ 905 16 890 891 # CC OC
+ 906 12 890 884 # CC CT1
+
+Angle Coeffs
+
+ 1 52 112.3 0 0 # C CP1 CP2
+ 2 50 112 0 0 # C CP1 HB
+ 3 50 108.2 0 0 # C CP1 N
+ 4 52 108 0 0 # C CT1 CT1
+ 5 52 108 0 0 # C CT1 CT2
+ 6 52 108 0 0 # C CT1 CT3
+ 7 50 109.5 0 0 # C CT1 HB
+ 8 50 107 0 0 # C CT1 NH1
+ 9 43.7 110 0 0 # C CT1 NH3
+ 10 50 109.5 0 0 # C CT2 HB
+ 11 50 107 0 0 # C CT2 NH1
+ 12 60 117 0 0 # C N CP1
+ 13 60 117 0 0 # C N CP3
+ 14 62.3 120 0 0 # C NC2 CT2
+ 15 49 120 0 0 # C NC2 HC
+ 16 50 120 0 0 # C NH1 CT1
+ 17 50 120 0 0 # C NH1 CT2
+ 18 34 123 0 0 # C NH1 H
+ 19 40 120 35 2.4162 # CA CA CA
+ 20 45.8 122.3 0 0 # CA CA CT2
+ 21 30 120 22 2.1525 # CA CA HP
+ 22 45.2 120 0 0 # CA CA OH1
+ 23 51.8 107.5 0 0 # CA CT2 CT1
+ 24 49.3 107.5 0 0 # CA CT2 HA
+ 25 65 108 0 0 # CA OH1 H
+ 26 52 108 0 0 # CC CT1 CT3
+ 27 50 109.5 0 0 # CC CT1 HB
+ 28 50 107 0 0 # CC CT1 NH1
+ 29 52 108 0 0 # CC CT2 CT1
+ 30 52 108 0 0 # CC CT2 CT2
+ 31 33 109.5 30 2.163 # CC CT2 HA
+ 32 50 120 0 0 # CC NH2 H
+ 33 20 112.5 0 0 # CP1 C N
+ 34 80 116.5 0 0 # CP1 C NH1
+ 35 80 118 0 0 # CP1 C O
+ 36 70 108.5 0 0 # CP1 CP2 CP2
+ 37 33.43 110.1 22.53 2.179 # CP1 CP2 HA
+ 38 100 114.2 0 0 # CP1 N CP3
+ 39 35 118 0 0 # CP2 CP1 HB
+ 40 70 110.8 0 0 # CP2 CP1 N
+ 41 70 108.5 0 0 # CP2 CP2 CP3
+ 42 26.5 110.1 22.53 2.179 # CP2 CP2 HA
+ 43 26.5 110.1 22.53 2.179 # CP2 CP3 HA
+ 44 70 110.5 0 0 # CP2 CP3 N
+ 45 26.5 110.1 22.53 2.179 # CP3 CP2 HA
+ 46 20 112.5 0 0 # CT1 C N
+ 47 80 116.5 0 0 # CT1 C NH1
+ 48 80 121 0 0 # CT1 C O
+ 49 40 118 50 2.388 # CT1 CC OC
+ 50 53.35 111 8 2.561 # CT1 CT1 CT2
+ 51 53.35 108.5 8 2.561 # CT1 CT1 CT3
+ 52 34.5 110.1 22.53 2.179 # CT1 CT1 HA
+ 53 35 111 0 0 # CT1 CT1 HB
+ 54 70 113.5 0 0 # CT1 CT1 NH1
+ 55 75.7 110.1 0 0 # CT1 CT1 OH1
+ 56 58.35 113.5 11.16 2.561 # CT1 CT2 CT1
+ 57 58.35 113.5 11.16 2.561 # CT1 CT2 CT2
+ 58 58.35 113.5 11.16 2.561 # CT1 CT2 CT3
+ 59 33.43 110.1 22.53 2.179 # CT1 CT2 HA
+ 60 75.7 110.1 0 0 # CT1 CT2 OH1
+ 61 58 112.5 0 0 # CT1 CT2 SM
+ 62 33.43 110.1 22.53 2.179 # CT1 CT3 HA
+ 63 35 117 0 0 # CT1 NH1 H
+ 64 30 109.5 20 2.074 # CT1 NH3 HC
+ 65 57.5 106 0 0 # CT1 OH1 H
+ 66 20 112.5 0 0 # CT2 C N
+ 67 80 116.5 0 0 # CT2 C NH1
+ 68 80 121 0 0 # CT2 C O
+ 69 50 116.5 50 2.45 # CT2 CC NH2
+ 70 15 121 50 2.44 # CT2 CC O
+ 71 40 118 50 2.388 # CT2 CC OC
+ 72 53.35 114 8 2.561 # CT2 CT1 CT3
+ 73 34.5 110.1 22.53 2.179 # CT2 CT1 HA
+ 74 35 111 0 0 # CT2 CT1 HB
+ 75 70 113.5 0 0 # CT2 CT1 NH1
+ 76 67.7 110 0 0 # CT2 CT1 NH3
+ 77 58.35 113.6 11.16 2.561 # CT2 CT2 CT2
+ 78 26.5 110.1 22.53 2.179 # CT2 CT2 HA
+ 79 67.7 107.5 0 0 # CT2 CT2 NC2
+ 80 67.7 110 0 0 # CT2 CT2 NH3
+ 81 58 114.5 0 0 # CT2 CT2 S
+ 82 34.6 110.1 22.53 2.179 # CT2 CT3 HA
+ 83 40.4 120 0 0 # CT2 NC2 HC
+ 84 35 117 0 0 # CT2 NH1 H
+ 85 30 109.5 20 2.074 # CT2 NH3 HC
+ 86 57.5 106 0 0 # CT2 OH1 H
+ 87 34 95 0 0 # CT2 S CT3
+ 88 72.5 103.3 0 0 # CT2 SM SM
+ 89 53.35 114 8 2.561 # CT3 CT1 CT3
+ 90 34.5 110.1 22.53 2.179 # CT3 CT1 HA
+ 91 35 111 0 0 # CT3 CT1 HB
+ 92 70 113.5 0 0 # CT3 CT1 NH1
+ 93 75.7 110.1 0 0 # CT3 CT1 OH1
+ 94 34.6 110.1 22.53 2.179 # CT3 CT2 HA
+ 95 23 120 0 0 # H NH2 H
+ 96 35.5 109 5.4 1.802 # HA CP2 HA
+ 97 35.5 109 5.4 1.802 # HA CP3 HA
+ 98 48 108 0 0 # HA CP3 N
+ 99 45.9 108.89 0 0 # HA CT1 OH1
+ 100 35.5 109 5.4 1.802 # HA CT2 HA
+ 101 51.5 107.5 0 0 # HA CT2 NC2
+ 102 45 107.5 35 2.101 # HA CT2 NH3
+ 103 45.9 108.89 0 0 # HA CT2 OH1
+ 104 46.1 111.3 0 0 # HA CT2 S
+ 105 38 111 0 0 # HA CT2 SM
+ 106 35.5 108.4 5.4 1.802 # HA CT3 HA
+ 107 46.1 111.3 0 0 # HA CT3 S
+ 108 48 112 0 0 # HB CP1 N
+ 109 48 108 0 0 # HB CT1 NH1
+ 110 51.5 107.5 0 0 # HB CT1 NH3
+ 111 36 115 0 0 # HB CT2 HB
+ 112 48 108 0 0 # HB CT2 NH1
+ 113 25 120 0 0 # HC NC2 HC
+ 114 44 109.5 0 0 # HC NH3 HC
+ 115 55 104.52 0 0 # HT OT HT
+ 116 80 122.5 0 0 # N C O
+ 117 52 120 90 2.3642 # NC2 C NC2
+ 118 80 122.5 0 0 # NH1 C O
+ 119 75 122.5 50 2.37 # NH2 CC O
+ 120 100 124 70 2.225 # OC CC OC
+
+Angles
+
+ 1 110 1 5 6 # HB CT1 NH3
+ 2 9 1 5 25 # C CT1 NH3
+ 3 64 2 1 5 # CT1 NH3 HC
+ 4 114 2 1 4 # HC NH3 HC
+ 5 114 2 1 3 # HC NH3 HC
+ 6 64 3 1 5 # CT1 NH3 HC
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+ 8 64 4 1 5 # CT1 NH3 HC
+ 9 48 5 25 26 # CT1 C O
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+ 12 59 5 7 8 # CT1 CT2 HA
+ 13 57 5 7 10 # CT1 CT2 CT2
+ 14 78 7 10 12 # CT2 CT2 HA
+ 15 78 7 10 11 # CT2 CT2 HA
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+ 24 78 10 7 9 # CT2 CT2 HA
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+ 29 78 13 10 12 # CT2 CT2 HA
+ 30 78 13 10 11 # CT2 CT2 HA
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+ 33 117 16 18 22 # NC2 C NC2
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+ 35 101 16 13 14 # HA CT2 NC2
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+ 37 15 18 22 23 # C NC2 HC
+ 38 15 18 16 17 # C NC2 HC
+ 39 15 20 19 18 # C NC2 HC
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+ 42 117 22 18 19 # NC2 C NC2
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+ 47 98 27 28 30 # HA CP3 N
+ 48 98 27 28 29 # HA CP3 N
+ 49 116 27 25 26 # N C O
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+ 51 45 28 36 37 # CP3 CP2 HA
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+ 55 34 31 39 41 # CP1 C NH1
+ 56 37 31 33 35 # CP1 CP2 HA
+ 57 37 31 33 34 # CP1 CP2 HA
+ 58 36 31 33 36 # CP1 CP2 CP2
+ 59 12 31 27 25 # C N CP1
+ 60 38 31 27 28 # CP1 N CP3
+ 61 42 33 36 38 # CP2 CP2 HA
+ 62 42 33 36 37 # CP2 CP2 HA
+ 63 41 33 36 28 # CP2 CP2 CP3
+ 64 39 33 31 32 # CP2 CP1 HB
+ 65 96 34 33 35 # HA CP2 HA
+ 66 42 36 33 35 # CP2 CP2 HA
+ 67 42 36 33 34 # CP2 CP2 HA
+ 68 43 36 28 30 # CP2 CP3 HA
+ 69 43 36 28 29 # CP2 CP3 HA
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+ 71 96 37 36 38 # HA CP2 HA
+ 72 2 39 31 32 # C CP1 HB
+ 73 1 39 31 33 # C CP1 CP2
+ 74 3 39 31 27 # C CP1 N
+ 75 109 41 43 44 # HB CT1 NH1
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+ 77 118 41 39 40 # NH1 C O
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+ 80 48 43 51 52 # CT1 C O
+ 81 47 43 51 53 # CT1 C NH1
+ 82 59 43 45 47 # CT1 CT2 HA
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+ 84 29 43 45 48 # CC CT2 CT1
+ 85 16 43 41 39 # C NH1 CT1
+ 86 71 45 48 49 # CT2 CC OC
+ 87 71 45 48 50 # CT2 CC OC
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+ 89 5 45 43 51 # C CT1 CT2
+ 90 75 45 43 41 # CT2 CT1 NH1
+ 91 100 46 45 47 # HA CT2 HA
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+ 93 31 48 45 46 # CC CT2 HA
+ 94 120 50 48 49 # OC CC OC
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+ 96 109 53 55 56 # HB CT1 NH1
+ 97 8 53 55 71 # C CT1 NH1
+ 98 118 53 51 52 # NH1 C O
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+ 101 48 55 71 72 # CT1 C O
+ 102 47 55 71 73 # CT1 C NH1
+ 103 59 55 57 59 # CT1 CT2 HA
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+ 107 20 57 60 61 # CA CA CT2
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+ 109 74 57 55 56 # CT2 CT1 HB
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+ 113 19 60 67 69 # CA CA CA
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+ 138 47 75 81 83 # CT1 C NH1
+ 139 59 75 77 79 # CT1 CT2 HA
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+ 141 61 75 77 80 # CT1 CT2 SM
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+ 143 88 77 80 865 # CT2 SM SM
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+ 145 5 77 75 81 # C CT1 CT2
+ 146 75 77 75 73 # CT2 CT1 NH1
+ 147 100 78 77 79 # HA CT2 HA
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+ 152 109 83 85 86 # HB CT1 NH1
+ 153 8 83 85 100 # C CT1 NH1
+ 154 118 83 81 82 # NH1 C O
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+ 159 59 85 87 89 # CT1 CT2 HA
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+ 161 56 85 87 90 # CT1 CT2 CT1
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+ 163 73 87 90 91 # CT2 CT1 HA
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+ 165 72 87 90 92 # CT2 CT1 CT3
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+ 172 62 90 96 97 # CT1 CT3 HA
+ 173 62 90 92 95 # CT1 CT3 HA
+ 174 62 90 92 94 # CT1 CT3 HA
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+ 179 89 92 90 96 # CT3 CT1 CT3
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+ 188 109 102 104 105 # HB CT1 NH1
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+ 195 59 104 106 108 # CT1 CT2 HA
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+ 207 71 109 112 114 # CT2 CC OC
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+ 215 108 117 121 122 # HB CP1 N
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+ 217 98 117 118 120 # HA CP3 N
+ 218 98 117 118 119 # HA CP3 N
+ 219 116 117 115 116 # N C O
+ 220 45 118 126 128 # CP3 CP2 HA
+ 221 45 118 126 127 # CP3 CP2 HA
+ 222 13 118 117 115 # C N CP3
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+ 224 35 121 129 130 # CP1 C O
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+ 226 37 121 123 125 # CP1 CP2 HA
+ 227 37 121 123 124 # CP1 CP2 HA
+ 228 36 121 123 126 # CP1 CP2 CP2
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+ 230 38 121 117 118 # CP1 N CP3
+ 231 42 123 126 128 # CP2 CP2 HA
+ 232 42 123 126 127 # CP2 CP2 HA
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+ 234 39 123 121 122 # CP2 CP1 HB
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+ 238 43 126 118 120 # CP2 CP3 HA
+ 239 43 126 118 119 # CP2 CP3 HA
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+ 245 108 131 135 136 # HB CP1 N
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+ 247 98 131 132 134 # HA CP3 N
+ 248 98 131 132 133 # HA CP3 N
+ 249 116 131 129 130 # N C O
+ 250 45 132 140 142 # CP3 CP2 HA
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+ 255 34 135 143 145 # CP1 C NH1
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+ 259 12 135 131 129 # C N CP1
+ 260 38 135 131 132 # CP1 N CP3
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+ 262 42 137 140 141 # CP2 CP2 HA
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+ 269 43 140 132 133 # CP2 CP3 HA
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+ 312 109 166 168 169 # HB CT1 NH1
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+ 314 118 166 164 165 # NH1 C O
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+ 317 48 168 178 179 # CT1 C O
+ 318 47 168 178 180 # CT1 C NH1
+ 319 52 168 170 171 # CT1 CT1 HA
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+ 321 55 168 170 172 # CT1 CT1 OH1
+ 322 16 168 166 164 # C NH1 CT1
+ 323 62 170 174 177 # CT1 CT3 HA
+ 324 62 170 174 176 # CT1 CT3 HA
+ 325 62 170 174 175 # CT1 CT3 HA
+ 326 65 170 172 173 # CT1 OH1 H
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+ 328 4 170 168 178 # C CT1 CT1
+ 329 54 170 168 166 # CT1 CT1 NH1
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+ 331 93 172 170 174 # CT3 CT1 OH1
+ 332 90 174 170 171 # CT3 CT1 HA
+ 333 106 175 174 177 # HA CT3 HA
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+ 336 7 178 168 169 # C CT1 HB
+ 337 112 180 182 184 # HB CT2 NH1
+ 338 112 180 182 183 # HB CT2 NH1
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+ 340 118 180 178 179 # NH1 C O
+ 341 18 181 180 178 # C NH1 H
+ 342 84 181 180 182 # CT2 NH1 H
+ 343 68 182 185 186 # CT2 C O
+ 344 66 182 185 187 # CT2 C N
+ 345 17 182 180 178 # C NH1 CT2
+ 346 111 183 182 184 # HB CT2 HB
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+ 348 10 185 182 183 # C CT2 HB
+ 349 108 187 191 192 # HB CP1 N
+ 350 40 187 191 193 # CP2 CP1 N
+ 351 98 187 188 190 # HA CP3 N
+ 352 98 187 188 189 # HA CP3 N
+ 353 116 187 185 186 # N C O
+ 354 45 188 196 198 # CP3 CP2 HA
+ 355 45 188 196 197 # CP3 CP2 HA
+ 356 13 188 187 185 # C N CP3
+ 357 97 189 188 190 # HA CP3 HA
+ 358 35 191 199 200 # CP1 C O
+ 359 34 191 199 201 # CP1 C NH1
+ 360 37 191 193 195 # CP1 CP2 HA
+ 361 37 191 193 194 # CP1 CP2 HA
+ 362 36 191 193 196 # CP1 CP2 CP2
+ 363 12 191 187 185 # C N CP1
+ 364 38 191 187 188 # CP1 N CP3
+ 365 42 193 196 198 # CP2 CP2 HA
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+ 368 39 193 191 192 # CP2 CP1 HB
+ 369 96 194 193 195 # HA CP2 HA
+ 370 42 196 193 195 # CP2 CP2 HA
+ 371 42 196 193 194 # CP2 CP2 HA
+ 372 43 196 188 190 # CP2 CP3 HA
+ 373 43 196 188 189 # CP2 CP3 HA
+ 374 44 196 188 187 # CP2 CP3 N
+ 375 96 197 196 198 # HA CP2 HA
+ 376 2 199 191 192 # C CP1 HB
+ 377 1 199 191 193 # C CP1 CP2
+ 378 3 199 191 187 # C CP1 N
+ 379 109 201 203 204 # HB CT1 NH1
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+ 381 118 201 199 200 # NH1 C O
+ 382 18 202 201 199 # C NH1 H
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+ 384 48 203 209 210 # CT1 C O
+ 385 47 203 209 211 # CT1 C NH1
+ 386 59 203 205 207 # CT1 CT2 HA
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+ 388 61 203 205 208 # CT1 CT2 SM
+ 389 16 203 201 199 # C NH1 CT1
+ 390 88 205 208 592 # CT2 SM SM
+ 391 74 205 203 204 # CT2 CT1 HB
+ 392 5 205 203 209 # C CT1 CT2
+ 393 75 205 203 201 # CT2 CT1 NH1
+ 394 100 206 205 207 # HA CT2 HA
+ 395 88 208 592 589 # CT2 SM SM
+ 396 105 208 205 207 # HA CT2 SM
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+ 1471 18 804 803 801 # C NH1 H
+ 1472 63 804 803 805 # CT1 NH1 H
+ 1473 48 805 818 819 # CT1 C O
+ 1474 47 805 818 820 # CT1 C NH1
+ 1475 59 805 807 809 # CT1 CT2 HA
+ 1476 59 805 807 808 # CT1 CT2 HA
+ 1477 57 805 807 810 # CT1 CT2 CT2
+ 1478 16 805 803 801 # C NH1 CT1
+ 1479 78 807 810 812 # CT2 CT2 HA
+ 1480 78 807 810 811 # CT2 CT2 HA
+ 1481 81 807 810 813 # CT2 CT2 S
+ 1482 74 807 805 806 # CT2 CT1 HB
+ 1483 5 807 805 818 # C CT1 CT2
+ 1484 75 807 805 803 # CT2 CT1 NH1
+ 1485 100 808 807 809 # HA CT2 HA
+ 1486 87 810 813 814 # CT2 S CT3
+ 1487 78 810 807 809 # CT2 CT2 HA
+ 1488 78 810 807 808 # CT2 CT2 HA
+ 1489 100 811 810 812 # HA CT2 HA
+ 1490 107 813 814 817 # HA CT3 S
+ 1491 107 813 814 816 # HA CT3 S
+ 1492 107 813 814 815 # HA CT3 S
+ 1493 104 813 810 812 # HA CT2 S
+ 1494 104 813 810 811 # HA CT2 S
+ 1495 106 815 814 817 # HA CT3 HA
+ 1496 106 815 814 816 # HA CT3 HA
+ 1497 106 816 814 817 # HA CT3 HA
+ 1498 7 818 805 806 # C CT1 HB
+ 1499 109 820 822 823 # HB CT1 NH1
+ 1500 8 820 822 842 # C CT1 NH1
+ 1501 118 820 818 819 # NH1 C O
+ 1502 18 821 820 818 # C NH1 H
+ 1503 63 821 820 822 # CT1 NH1 H
+ 1504 48 822 842 843 # CT1 C O
+ 1505 47 822 842 844 # CT1 C NH1
+ 1506 59 822 824 826 # CT1 CT2 HA
+ 1507 59 822 824 825 # CT1 CT2 HA
+ 1508 57 822 824 827 # CT1 CT2 CT2
+ 1509 16 822 820 818 # C NH1 CT1
+ 1510 78 824 827 829 # CT2 CT2 HA
+ 1511 78 824 827 828 # CT2 CT2 HA
+ 1512 77 824 827 830 # CT2 CT2 CT2
+ 1513 74 824 822 823 # CT2 CT1 HB
+ 1514 5 824 822 842 # C CT1 CT2
+ 1515 75 824 822 820 # CT2 CT1 NH1
+ 1516 100 825 824 826 # HA CT2 HA
+ 1517 78 827 830 832 # CT2 CT2 HA
+ 1518 78 827 830 831 # CT2 CT2 HA
+ 1519 79 827 830 833 # CT2 CT2 NC2
+ 1520 78 827 824 826 # CT2 CT2 HA
+ 1521 78 827 824 825 # CT2 CT2 HA
+ 1522 100 828 827 829 # HA CT2 HA
+ 1523 83 830 833 834 # CT2 NC2 HC
+ 1524 14 830 833 835 # C NC2 CT2
+ 1525 78 830 827 829 # CT2 CT2 HA
+ 1526 78 830 827 828 # CT2 CT2 HA
+ 1527 100 831 830 832 # HA CT2 HA
+ 1528 117 833 835 836 # NC2 C NC2
+ 1529 117 833 835 839 # NC2 C NC2
+ 1530 101 833 830 832 # HA CT2 NC2
+ 1531 101 833 830 831 # HA CT2 NC2
+ 1532 15 835 839 841 # C NC2 HC
+ 1533 15 835 839 840 # C NC2 HC
+ 1534 15 835 833 834 # C NC2 HC
+ 1535 15 837 836 835 # C NC2 HC
+ 1536 113 837 836 838 # HC NC2 HC
+ 1537 15 838 836 835 # C NC2 HC
+ 1538 117 839 835 836 # NC2 C NC2
+ 1539 113 840 839 841 # HC NC2 HC
+ 1540 7 842 822 823 # C CT1 HB
+ 1541 109 844 846 847 # HB CT1 NH1
+ 1542 8 844 846 856 # C CT1 NH1
+ 1543 118 844 842 843 # NH1 C O
+ 1544 18 845 844 842 # C NH1 H
+ 1545 63 845 844 846 # CT1 NH1 H
+ 1546 48 846 856 857 # CT1 C O
+ 1547 47 846 856 858 # CT1 C NH1
+ 1548 52 846 848 849 # CT1 CT1 HA
+ 1549 51 846 848 852 # CT1 CT1 CT3
+ 1550 55 846 848 850 # CT1 CT1 OH1
+ 1551 16 846 844 842 # C NH1 CT1
+ 1552 62 848 852 855 # CT1 CT3 HA
+ 1553 62 848 852 854 # CT1 CT3 HA
+ 1554 62 848 852 853 # CT1 CT3 HA
+ 1555 65 848 850 851 # CT1 OH1 H
+ 1556 53 848 846 847 # CT1 CT1 HB
+ 1557 4 848 846 856 # C CT1 CT1
+ 1558 54 848 846 844 # CT1 CT1 NH1
+ 1559 99 850 848 849 # HA CT1 OH1
+ 1560 93 850 848 852 # CT3 CT1 OH1
+ 1561 90 852 848 849 # CT3 CT1 HA
+ 1562 106 853 852 855 # HA CT3 HA
+ 1563 106 853 852 854 # HA CT3 HA
+ 1564 106 854 852 855 # HA CT3 HA
+ 1565 7 856 846 847 # C CT1 HB
+ 1566 109 858 860 861 # HB CT1 NH1
+ 1567 8 858 860 866 # C CT1 NH1
+ 1568 118 858 856 857 # NH1 C O
+ 1569 18 859 858 856 # C NH1 H
+ 1570 63 859 858 860 # CT1 NH1 H
+ 1571 48 860 866 867 # CT1 C O
+ 1572 47 860 866 868 # CT1 C NH1
+ 1573 59 860 862 864 # CT1 CT2 HA
+ 1574 59 860 862 863 # CT1 CT2 HA
+ 1575 61 860 862 865 # CT1 CT2 SM
+ 1576 16 860 858 856 # C NH1 CT1
+ 1577 74 862 860 861 # CT2 CT1 HB
+ 1578 5 862 860 866 # C CT1 CT2
+ 1579 75 862 860 858 # CT2 CT1 NH1
+ 1580 100 863 862 864 # HA CT2 HA
+ 1581 105 865 862 864 # HA CT2 SM
+ 1582 105 865 862 863 # HA CT2 SM
+ 1583 7 866 860 861 # C CT1 HB
+ 1584 112 868 870 872 # HB CT2 NH1
+ 1585 112 868 870 871 # HB CT2 NH1
+ 1586 11 868 870 873 # C CT2 NH1
+ 1587 118 868 866 867 # NH1 C O
+ 1588 18 869 868 866 # C NH1 H
+ 1589 84 869 868 870 # CT2 NH1 H
+ 1590 68 870 873 874 # CT2 C O
+ 1591 67 870 873 875 # CT2 C NH1
+ 1592 17 870 868 866 # C NH1 CT2
+ 1593 111 871 870 872 # HB CT2 HB
+ 1594 10 873 870 872 # C CT2 HB
+ 1595 10 873 870 871 # C CT2 HB
+ 1596 112 875 877 879 # HB CT2 NH1
+ 1597 112 875 877 878 # HB CT2 NH1
+ 1598 11 875 877 880 # C CT2 NH1
+ 1599 118 875 873 874 # NH1 C O
+ 1600 18 876 875 873 # C NH1 H
+ 1601 84 876 875 877 # CT2 NH1 H
+ 1602 68 877 880 881 # CT2 C O
+ 1603 67 877 880 882 # CT2 C NH1
+ 1604 17 877 875 873 # C NH1 CT2
+ 1605 111 878 877 879 # HB CT2 HB
+ 1606 10 880 877 879 # C CT2 HB
+ 1607 10 880 877 878 # C CT2 HB
+ 1608 109 882 884 885 # HB CT1 NH1
+ 1609 28 882 884 890 # CC CT1 NH1
+ 1610 118 882 880 881 # NH1 C O
+ 1611 18 883 882 880 # C NH1 H
+ 1612 63 883 882 884 # CT1 NH1 H
+ 1613 62 884 886 889 # CT1 CT3 HA
+ 1614 62 884 886 888 # CT1 CT3 HA
+ 1615 62 884 886 887 # CT1 CT3 HA
+ 1616 16 884 882 880 # C NH1 CT1
+ 1617 91 886 884 885 # CT3 CT1 HB
+ 1618 26 886 884 890 # CC CT1 CT3
+ 1619 92 886 884 882 # CT3 CT1 NH1
+ 1620 106 887 886 889 # HA CT3 HA
+ 1621 106 887 886 888 # HA CT3 HA
+ 1622 106 888 886 889 # HA CT3 HA
+ 1623 27 890 884 885 # CC CT1 HB
+ 1624 49 891 890 884 # CT1 CC OC
+ 1625 49 892 890 884 # CT1 CC OC
+ 1626 120 892 890 891 # OC CC OC
+
+Dihedral Coeffs
+
+1 0.14 3 0 0 # C CP1 CP2 CP2
+2 0.14 3 0 0 # C CP1 CP2 HA
+3 0.8 3 0 0 # C CP1 N C
+4 0.1 3 0 0 # C CP1 N CP3
+5 0.2 3 0 0 # C CT1 CT1 CT2
+6 0.2 3 0 0 # C CT1 CT1 CT3
+7 0.2 3 0 0 # C CT1 CT1 HA
+8 0.2 3 0 0 # C CT1 CT1 OH1
+9 0.04 3 0 0 # C CT1 CT2 CA
+10 0.2 3 0 0 # C CT1 CT2 CC
+11 0.2 3 0 0 # C CT1 CT2 CT1
+12 0.2 3 0 0 # C CT1 CT2 CT2
+13 0.2 3 0 0 # C CT1 CT2 HA
+14 0.2 3 0 0 # C CT1 CT2 OH1
+15 0.2 3 0 0 # C CT1 CT2 SM
+16 0.2 3 0 0 # C CT1 CT3 HA
+17 0.2 1 180 0 # C CT1 NH1 C
+18 0 1 0 0 # C CT1 NH1 H
+19 0.1 3 0 0 # C CT1 NH3 HC
+20 0.2 1 180 0 # C CT2 NH1 C
+21 0 1 0 0 # C CT2 NH1 H
+22 0.8 3 0 0 # C N CP1 CP2
+23 0.8 3 0 0 # C N CP1 HB
+24 0 3 180 0 # C N CP3 CP2
+25 0 3 180 0 # C N CP3 HA
+26 0 6 180 0 # C NC2 CT2 CT2
+27 0 6 180 0 # C NC2 CT2 HA
+28 0.2 1 180 0 # C NH1 CT1 CC
+29 1.8 1 0 0 # C NH1 CT1 CT1
+30 1.8 1 0 0 # C NH1 CT1 CT2
+31 1.8 1 0 0 # C NH1 CT1 CT3
+32 0 1 0 0 # C NH1 CT1 HB
+33 0 1 0 0 # C NH1 CT2 HB
+34 3.1 2 180 0 # CA CA CA CA
+35 3.1 2 180 0 # CA CA CA CT2
+36 4.2 2 180 0 # CA CA CA HP
+37 3.1 2 180 0 # CA CA CA OH1
+38 0.23 2 180 0 # CA CA CT2 CT1
+39 0 6 0 0 # CA CA CT2 HA
+40 0.99 2 180 0 # CA CA OH1 H
+41 0.2 3 0 0 # CA CT2 CT1 HB
+42 0.2 3 0 0 # CA CT2 CT1 NH1
+43 0.2 3 0 0 # CC CT1 CT3 HA
+44 0 1 0 0 # CC CT1 NH1 H
+45 0.2 3 0 0 # CC CT2 CT1 HB
+46 0.2 3 0 0 # CC CT2 CT1 NH1
+47 0.195 3 0 0 # CC CT2 CT2 CT1
+48 0.195 3 0 0 # CC CT2 CT2 HA
+49 2.75 2 180 0 # CP1 C N CP1
+50 0.3 4 0 0 # CP1 C N CP1
+51 2.75 2 180 0 # CP1 C N CP3
+52 0.3 4 0 0 # CP1 C N CP3
+53 1.6 1 0 0 # CP1 C NH1 CT1
+54 2.5 2 180 0 # CP1 C NH1 CT1
+55 2.5 2 180 0 # CP1 C NH1 H
+56 0.16 3 0 0 # CP1 CP2 CP2 CP3
+57 0.16 3 0 0 # CP1 CP2 CP2 HA
+58 2.75 2 180 0 # CP1 N C CT1
+59 0.3 4 0 0 # CP1 N C CT1
+60 2.75 2 180 0 # CP1 N C CT2
+61 0.3 4 0 0 # CP1 N C CT2
+62 2.75 2 180 0 # CP1 N C O
+63 0.3 4 0 0 # CP1 N C O
+64 0.1 3 0 0 # CP1 N CP3 CP2
+65 0.1 3 0 0 # CP1 N CP3 HA
+66 0.4 1 0 0 # CP2 CP1 C N
+67 0.6 2 0 0 # CP2 CP1 C N
+68 0.4 1 0 0 # CP2 CP1 C NH1
+69 0.6 2 0 0 # CP2 CP1 C NH1
+70 0.4 1 180 0 # CP2 CP1 C O
+71 0.6 2 0 0 # CP2 CP1 C O
+72 0.1 3 0 0 # CP2 CP1 N CP3
+73 0.14 3 0 0 # CP2 CP2 CP1 HB
+74 0.14 3 0 0 # CP2 CP2 CP1 N
+75 0.14 3 0 0 # CP2 CP2 CP3 HA
+76 0.14 3 0 0 # CP2 CP2 CP3 N
+77 0.16 3 0 0 # CP3 CP2 CP2 HA
+78 2.75 2 180 0 # CP3 N C CT1
+79 0.3 4 0 0 # CP3 N C CT1
+80 2.75 2 180 0 # CP3 N C CT2
+81 0.3 4 0 0 # CP3 N C CT2
+82 2.75 2 180 0 # CP3 N C O
+83 0.3 4 0 0 # CP3 N C O
+84 0.1 3 0 0 # CP3 N CP1 HB
+85 1.6 1 0 0 # CT1 C NH1 CT1
+86 2.5 2 180 0 # CT1 C NH1 CT1
+87 1.6 1 0 0 # CT1 C NH1 CT2
+88 2.5 2 180 0 # CT1 C NH1 CT2
+89 2.5 2 180 0 # CT1 C NH1 H
+90 0 1 0 0 # CT1 CT1 C NH1
+91 1.4 1 0 0 # CT1 CT1 C O
+92 0.2 3 0 0 # CT1 CT1 CT2 CT3
+93 0.2 3 0 0 # CT1 CT1 CT2 HA
+94 0.2 3 0 0 # CT1 CT1 CT3 HA
+95 0 1 0 0 # CT1 CT1 NH1 H
+96 1.33 1 0 0 # CT1 CT1 OH1 H
+97 0.18 2 0 0 # CT1 CT1 OH1 H
+98 0.32 3 0 0 # CT1 CT1 OH1 H
+99 0.05 6 180 0 # CT1 CT2 CC NH2
+100 0.05 6 180 0 # CT1 CT2 CC O
+101 0.05 6 180 0 # CT1 CT2 CC OC
+102 0.2 3 0 0 # CT1 CT2 CT1 CT3
+103 0.2 3 0 0 # CT1 CT2 CT1 HA
+104 0.2 3 0 0 # CT1 CT2 CT1 HB
+105 0.2 3 0 0 # CT1 CT2 CT1 NH1
+106 0.195 3 0 0 # CT1 CT2 CT2 CT2
+107 0.195 3 0 0 # CT1 CT2 CT2 HA
+108 0.195 3 0 0 # CT1 CT2 CT2 S
+109 0.16 3 0 0 # CT1 CT2 CT3 HA
+110 1.3 1 0 0 # CT1 CT2 OH1 H
+111 0.3 2 0 0 # CT1 CT2 OH1 H
+112 0.42 3 0 0 # CT1 CT2 OH1 H
+113 0.31 3 0 0 # CT1 CT2 SM SM
+114 1.6 1 0 0 # CT1 NH1 C CT2
+115 2.5 2 180 0 # CT1 NH1 C CT2
+116 2.5 2 180 0 # CT1 NH1 C O
+117 1.6 1 0 0 # CT2 C NH1 CT2
+118 2.5 2 180 0 # CT2 C NH1 CT2
+119 2.5 2 180 0 # CT2 C NH1 H
+120 4.2 2 180 0 # CT2 CA CA HP
+121 1.4 2 180 0 # CT2 CC NH2 H
+122 0 1 0 0 # CT2 CT1 C N
+123 0 1 0 0 # CT2 CT1 C NH1
+124 1.4 1 0 0 # CT2 CT1 C O
+125 0.2 3 0 0 # CT2 CT1 CT1 HB
+126 0.2 3 0 0 # CT2 CT1 CT1 NH1
+127 0.2 3 0 0 # CT2 CT1 CT3 HA
+128 0 1 0 0 # CT2 CT1 NH1 H
+129 0.1 3 0 0 # CT2 CT1 NH3 HC
+130 0.05 6 180 0 # CT2 CT2 CC NH2
+131 0.05 6 180 0 # CT2 CT2 CC O
+132 0.05 6 180 0 # CT2 CT2 CC OC
+133 0.2 3 0 0 # CT2 CT2 CT1 HB
+134 0.2 3 0 0 # CT2 CT2 CT1 NH1
+135 0.2 3 0 0 # CT2 CT2 CT1 NH3
+136 0.15 1 0 0 # CT2 CT2 CT2 CT2
+137 0.195 3 0 0 # CT2 CT2 CT2 HA
+138 0.195 3 0 0 # CT2 CT2 CT2 NC2
+139 0.195 3 0 0 # CT2 CT2 CT2 NH3
+140 0 6 180 0 # CT2 CT2 NC2 HC
+141 0.1 3 0 0 # CT2 CT2 NH3 HC
+142 0.24 1 180 0 # CT2 CT2 S CT3
+143 0.37 3 0 0 # CT2 CT2 S CT3
+144 2.25 2 180 0 # CT2 NC2 C NC2
+145 2.5 2 180 0 # CT2 NH1 C O
+146 0.28 3 0 0 # CT2 S CT3 HA
+147 1 1 0 0 # CT2 SM SM CT2
+148 4.1 2 0 0 # CT2 SM SM CT2
+149 0.9 3 0 0 # CT2 SM SM CT2
+150 0 1 0 0 # CT3 CT1 C NH1
+151 1.4 1 0 0 # CT3 CT1 C O
+152 0.05 6 180 0 # CT3 CT1 CC OC
+153 0.2 3 0 0 # CT3 CT1 CT1 HB
+154 0.2 3 0 0 # CT3 CT1 CT1 NH1
+155 0.2 3 0 0 # CT3 CT1 CT2 CT3
+156 0.2 3 0 0 # CT3 CT1 CT2 HA
+157 0.2 3 0 0 # CT3 CT1 CT3 HA
+158 0 1 0 0 # CT3 CT1 NH1 H
+159 1.33 1 0 0 # CT3 CT1 OH1 H
+160 0.18 2 0 0 # CT3 CT1 OH1 H
+161 0.32 3 0 0 # CT3 CT1 OH1 H
+162 0.2 3 0 0 # CT3 CT2 CT1 HA
+163 0.28 3 0 0 # CT3 S CT2 HA
+164 2.5 2 180 0 # H NH1 C O
+165 0 1 0 0 # H NH1 CT1 HB
+166 0 1 0 0 # H NH1 CT2 HB
+167 1.4 2 180 0 # H NH2 CC O
+168 0.14 3 0 0 # H OH1 CT1 HA
+169 0.14 3 0 0 # H OH1 CT2 HA
+170 0.14 3 0 0 # HA CP2 CP1 HB
+171 0.14 3 0 0 # HA CP2 CP1 N
+172 0.16 3 0 0 # HA CP2 CP2 HA
+173 0.14 3 0 0 # HA CP2 CP3 HA
+174 0.14 3 0 0 # HA CP2 CP3 N
+175 0.2 3 0 0 # HA CT1 CT1 HB
+176 0.2 3 0 0 # HA CT1 CT1 NH1
+177 0.2 3 0 0 # HA CT1 CT2 HA
+178 0.2 3 0 0 # HA CT1 CT3 HA
+179 0 3 180 0 # HA CT2 CC NH2
+180 0 3 180 0 # HA CT2 CC O
+181 0.05 6 180 0 # HA CT2 CC OC
+182 0.2 3 0 0 # HA CT2 CT1 HB
+183 0.2 3 0 0 # HA CT2 CT1 NH1
+184 0.2 3 0 0 # HA CT2 CT1 NH3
+185 0.195 3 0 0 # HA CT2 CT2 HA
+186 0.195 3 0 0 # HA CT2 CT2 NC2
+187 0.195 3 0 0 # HA CT2 CT2 NH3
+188 0.01 3 0 0 # HA CT2 CT2 S
+189 0.16 3 0 0 # HA CT2 CT3 HA
+190 0 6 180 0 # HA CT2 NC2 HC
+191 0.1 3 0 0 # HA CT2 NH3 HC
+192 0.158 3 0 0 # HA CT2 SM SM
+193 0.2 3 0 0 # HA CT3 CT1 HB
+194 0.2 3 0 0 # HA CT3 CT1 NH1
+195 0.2 3 0 0 # HA CT3 CT1 OH1
+196 0.4 1 180 0 # HB CP1 C N
+197 0.6 2 0 0 # HB CP1 C N
+198 0.4 1 180 0 # HB CP1 C NH1
+199 0.6 2 0 0 # HB CP1 C NH1
+200 0.4 1 0 0 # HB CP1 C O
+201 0.6 2 0 0 # HB CP1 C O
+202 0 1 0 0 # HB CT1 C N
+203 0 1 0 0 # HB CT1 C NH1
+204 0 1 0 0 # HB CT1 C O
+205 0.05 6 180 0 # HB CT1 CC OC
+206 0.2 3 0 0 # HB CT1 CT1 OH1
+207 0.2 3 0 0 # HB CT1 CT2 OH1
+208 0.2 3 0 0 # HB CT1 CT2 SM
+209 0.1 3 0 0 # HB CT1 NH3 HC
+210 0 1 0 0 # HB CT2 C N
+211 0 1 0 0 # HB CT2 C NH1
+212 0 1 0 0 # HB CT2 C O
+213 2.25 2 180 0 # HC NC2 C NC2
+214 2.4 2 180 0 # HP CA CA HP
+215 4.2 2 180 0 # HP CA CA OH1
+216 0.3 1 0 0 # N C CP1 N
+217 -0.3 4 0 0 # N C CP1 N
+218 0.4 1 0 0 # N C CT1 NH1
+219 0.4 1 0 0 # N C CT1 NH3
+220 0.4 1 0 0 # N C CT2 NH1
+221 0.3 1 0 0 # N CP1 C NH1
+222 -0.3 4 0 0 # N CP1 C NH1
+223 -0.3 4 0 0 # N CP1 C O
+224 0.6 1 0 0 # NH1 C CT1 NH1
+225 0.6 1 0 0 # NH1 C CT2 NH1
+226 0 1 0 0 # NH1 CT1 C O
+227 0.05 6 180 0 # NH1 CT1 CC OC
+228 0.2 3 0 0 # NH1 CT1 CT1 OH1
+229 0.2 3 0 0 # NH1 CT1 CT2 OH1
+230 0.2 3 0 0 # NH1 CT1 CT2 SM
+231 0 1 0 0 # NH1 CT2 C O
+232 0 1 0 0 # NH3 CT1 C O
+
+Dihedrals
+
+ 1 135 1 5 7 10 # CT2 CT2 CT1 NH3
+ 2 184 1 5 7 8 # HA CT2 CT1 NH3
+ 3 184 1 5 7 9 # HA CT2 CT1 NH3
+ 4 219 1 5 25 27 # N C CT1 NH3
+ 5 232 1 5 25 26 # NH3 CT1 C O
+ 6 129 2 1 5 7 # CT2 CT1 NH3 HC
+ 7 19 2 1 5 25 # C CT1 NH3 HC
+ 8 209 2 1 5 6 # HB CT1 NH3 HC
+ 9 129 3 1 5 7 # CT2 CT1 NH3 HC
+ 10 19 3 1 5 25 # C CT1 NH3 HC
+ 11 209 3 1 5 6 # HB CT1 NH3 HC
+ 12 129 4 1 5 7 # CT2 CT1 NH3 HC
+ 13 19 4 1 5 25 # C CT1 NH3 HC
+ 14 209 4 1 5 6 # HB CT1 NH3 HC
+ 15 58 5 25 27 31 # CP1 N C CT1
+ 16 59 5 25 27 31 # CP1 N C CT1
+ 17 78 5 25 27 28 # CP3 N C CT1
+ 18 79 5 25 27 28 # CP3 N C CT1
+ 19 106 5 7 10 13 # CT1 CT2 CT2 CT2
+ 20 107 5 7 10 11 # CT1 CT2 CT2 HA
+ 21 107 5 7 10 12 # CT1 CT2 CT2 HA
+ 22 133 6 5 7 10 # CT2 CT2 CT1 HB
+ 23 182 6 5 7 8 # HA CT2 CT1 HB
+ 24 182 6 5 7 9 # HA CT2 CT1 HB
+ 25 202 6 5 25 27 # HB CT1 C N
+ 26 204 6 5 25 26 # HB CT1 C O
+ 27 138 7 10 13 16 # CT2 CT2 CT2 NC2
+ 28 137 7 10 13 14 # CT2 CT2 CT2 HA
+ 29 137 7 10 13 15 # CT2 CT2 CT2 HA
+ 30 122 7 5 25 27 # CT2 CT1 C N
+ 31 124 7 5 25 26 # CT2 CT1 C O
+ 32 13 8 7 5 25 # C CT1 CT2 HA
+ 33 137 8 7 10 13 # CT2 CT2 CT2 HA
+ 34 185 8 7 10 11 # HA CT2 CT2 HA
+ 35 185 8 7 10 12 # HA CT2 CT2 HA
+ 36 13 9 7 5 25 # C CT1 CT2 HA
+ 37 137 9 7 10 13 # CT2 CT2 CT2 HA
+ 38 185 9 7 10 11 # HA CT2 CT2 HA
+ 39 185 9 7 10 12 # HA CT2 CT2 HA
+ 40 26 10 13 16 18 # C NC2 CT2 CT2
+ 41 140 10 13 16 17 # CT2 CT2 NC2 HC
+ 42 12 10 7 5 25 # C CT1 CT2 CT2
+ 43 186 11 10 13 16 # HA CT2 CT2 NC2
+ 44 185 11 10 13 14 # HA CT2 CT2 HA
+ 45 185 11 10 13 15 # HA CT2 CT2 HA
+ 46 186 12 10 13 16 # HA CT2 CT2 NC2
+ 47 185 12 10 13 14 # HA CT2 CT2 HA
+ 48 185 12 10 13 15 # HA CT2 CT2 HA
+ 49 144 13 16 18 22 # CT2 NC2 C NC2
+ 50 144 13 16 18 19 # CT2 NC2 C NC2
+ 51 27 14 13 16 18 # C NC2 CT2 HA
+ 52 190 14 13 16 17 # HA CT2 NC2 HC
+ 53 27 15 13 16 18 # C NC2 CT2 HA
+ 54 190 15 13 16 17 # HA CT2 NC2 HC
+ 55 213 16 18 22 23 # HC NC2 C NC2
+ 56 213 16 18 22 24 # HC NC2 C NC2
+ 57 213 16 18 19 20 # HC NC2 C NC2
+ 58 213 16 18 19 21 # HC NC2 C NC2
+ 59 213 17 16 18 22 # HC NC2 C NC2
+ 60 213 17 16 18 19 # HC NC2 C NC2
+ 61 213 19 18 22 23 # HC NC2 C NC2
+ 62 213 19 18 22 24 # HC NC2 C NC2
+ 63 213 20 19 18 22 # HC NC2 C NC2
+ 64 213 21 19 18 22 # HC NC2 C NC2
+ 65 3 25 27 31 39 # C CP1 N C
+ 66 22 25 27 31 33 # C N CP1 CP2
+ 67 23 25 27 31 32 # C N CP1 HB
+ 68 24 25 27 28 36 # C N CP3 CP2
+ 69 25 25 27 28 29 # C N CP3 HA
+ 70 25 25 27 28 30 # C N CP3 HA
+ 71 62 26 25 27 31 # CP1 N C O
+ 72 63 26 25 27 31 # CP1 N C O
+ 73 82 26 25 27 28 # CP3 N C O
+ 74 83 26 25 27 28 # CP3 N C O
+ 75 221 27 31 39 41 # N CP1 C NH1
+ 76 222 27 31 39 41 # N CP1 C NH1
+ 77 223 27 31 39 40 # N CP1 C O
+ 78 74 27 31 33 36 # CP2 CP2 CP1 N
+ 79 171 27 31 33 34 # HA CP2 CP1 N
+ 80 171 27 31 33 35 # HA CP2 CP1 N
+ 81 76 27 28 36 33 # CP2 CP2 CP3 N
+ 82 174 27 28 36 37 # HA CP2 CP3 N
+ 83 174 27 28 36 38 # HA CP2 CP3 N
+ 84 56 28 36 33 31 # CP1 CP2 CP2 CP3
+ 85 77 28 36 33 34 # CP3 CP2 CP2 HA
+ 86 77 28 36 33 35 # CP3 CP2 CP2 HA
+ 87 4 28 27 31 39 # C CP1 N CP3
+ 88 72 28 27 31 33 # CP2 CP1 N CP3
+ 89 84 28 27 31 32 # CP3 N CP1 HB
+ 90 75 29 28 36 33 # CP2 CP2 CP3 HA
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+ 1932 226 675 677 687 688 # NH1 CT1 C O
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+ 1938 86 677 687 689 691 # CT1 C NH1 CT1
+ 1939 99 677 679 682 684 # CT1 CT2 CC NH2
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+ 1944 203 678 677 687 689 # HB CT1 C NH1
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+ 1946 121 679 682 684 685 # CT2 CC NH2 H
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+ 1948 123 679 677 687 689 # CT2 CT1 C NH1
+ 1949 124 679 677 687 688 # CT2 CT1 C O
+ 1950 13 680 679 677 687 # C CT1 CT2 HA
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+ 1953 13 681 679 677 687 # C CT1 CT2 HA
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+ 1956 10 682 679 677 687 # C CT1 CT2 CC
+ 1957 167 683 682 684 685 # H NH2 CC O
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+ 1959 30 687 689 691 693 # C NH1 CT1 CT2
+ 1960 17 687 689 691 701 # C CT1 NH1 C
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+ 1962 164 688 687 689 690 # H NH1 C O
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+ 1965 183 689 691 693 694 # HA CT2 CT1 NH1
+ 1966 183 689 691 693 695 # HA CT2 CT1 NH1
+ 1967 224 689 691 701 703 # NH1 C CT1 NH1
+ 1968 226 689 691 701 702 # NH1 CT1 C O
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+ 1971 165 690 689 691 692 # H NH1 CT1 HB
+ 1972 89 691 701 703 704 # CT1 C NH1 H
+ 1973 85 691 701 703 705 # CT1 C NH1 CT1
+ 1974 86 691 701 703 705 # CT1 C NH1 CT1
+ 1975 99 691 693 696 698 # CT1 CT2 CC NH2
+ 1976 100 691 693 696 697 # CT1 CT2 CC O
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+ 1979 182 692 691 693 695 # HA CT2 CT1 HB
+ 1980 203 692 691 701 703 # HB CT1 C NH1
+ 1981 204 692 691 701 702 # HB CT1 C O
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+ 2378 164 843 842 844 845 # H NH1 C O
+ 2379 116 843 842 844 846 # CT1 NH1 C O
+ 2380 228 844 846 848 850 # NH1 CT1 CT1 OH1
+ 2381 154 844 846 848 852 # CT3 CT1 CT1 NH1
+ 2382 176 844 846 848 849 # HA CT1 CT1 NH1
+ 2383 224 844 846 856 858 # NH1 C CT1 NH1
+ 2384 226 844 846 856 857 # NH1 CT1 C O
+ 2385 95 845 844 846 848 # CT1 CT1 NH1 H
+ 2386 18 845 844 846 856 # C CT1 NH1 H
+ 2387 165 845 844 846 847 # H NH1 CT1 HB
+ 2388 89 846 856 858 859 # CT1 C NH1 H
+ 2389 85 846 856 858 860 # CT1 C NH1 CT1
+ 2390 86 846 856 858 860 # CT1 C NH1 CT1
+ 2391 96 846 848 850 851 # CT1 CT1 OH1 H
+ 2392 97 846 848 850 851 # CT1 CT1 OH1 H
+ 2393 98 846 848 850 851 # CT1 CT1 OH1 H
+ 2394 94 846 848 852 853 # CT1 CT1 CT3 HA
+ 2395 94 846 848 852 854 # CT1 CT1 CT3 HA
+ 2396 94 846 848 852 855 # CT1 CT1 CT3 HA
+ 2397 206 847 846 848 850 # HB CT1 CT1 OH1
+ 2398 153 847 846 848 852 # CT3 CT1 CT1 HB
+ 2399 175 847 846 848 849 # HA CT1 CT1 HB
+ 2400 203 847 846 856 858 # HB CT1 C NH1
+ 2401 204 847 846 856 857 # HB CT1 C O
+ 2402 90 848 846 856 858 # CT1 CT1 C NH1
+ 2403 91 848 846 856 857 # CT1 CT1 C O
+ 2404 7 849 848 846 856 # C CT1 CT1 HA
+ 2405 168 849 848 850 851 # H OH1 CT1 HA
+ 2406 178 849 848 852 853 # HA CT1 CT3 HA
+ 2407 178 849 848 852 854 # HA CT1 CT3 HA
+ 2408 178 849 848 852 855 # HA CT1 CT3 HA
+ 2409 8 850 848 846 856 # C CT1 CT1 OH1
+ 2410 195 850 848 852 853 # HA CT3 CT1 OH1
+ 2411 195 850 848 852 854 # HA CT3 CT1 OH1
+ 2412 195 850 848 852 855 # HA CT3 CT1 OH1
+ 2413 159 851 850 848 852 # CT3 CT1 OH1 H
+ 2414 160 851 850 848 852 # CT3 CT1 OH1 H
+ 2415 161 851 850 848 852 # CT3 CT1 OH1 H
+ 2416 6 852 848 846 856 # C CT1 CT1 CT3
+ 2417 30 856 858 860 862 # C NH1 CT1 CT2
+ 2418 17 856 858 860 866 # C CT1 NH1 C
+ 2419 32 856 858 860 861 # C NH1 CT1 HB
+ 2420 164 857 856 858 859 # H NH1 C O
+ 2421 116 857 856 858 860 # CT1 NH1 C O
+ 2422 230 858 860 862 865 # NH1 CT1 CT2 SM
+ 2423 183 858 860 862 863 # HA CT2 CT1 NH1
+ 2424 183 858 860 862 864 # HA CT2 CT1 NH1
+ 2425 224 858 860 866 868 # NH1 C CT1 NH1
+ 2426 226 858 860 866 867 # NH1 CT1 C O
+ 2427 128 859 858 860 862 # CT2 CT1 NH1 H
+ 2428 18 859 858 860 866 # C CT1 NH1 H
+ 2429 165 859 858 860 861 # H NH1 CT1 HB
+ 2430 89 860 866 868 869 # CT1 C NH1 H
+ 2431 87 860 866 868 870 # CT1 C NH1 CT2
+ 2432 88 860 866 868 870 # CT1 C NH1 CT2
+ 2433 208 861 860 862 865 # HB CT1 CT2 SM
+ 2434 182 861 860 862 863 # HA CT2 CT1 HB
+ 2435 182 861 860 862 864 # HA CT2 CT1 HB
+ 2436 203 861 860 866 868 # HB CT1 C NH1
+ 2437 204 861 860 866 867 # HB CT1 C O
+ 2438 123 862 860 866 868 # CT2 CT1 C NH1
+ 2439 124 862 860 866 867 # CT2 CT1 C O
+ 2440 192 863 862 865 80 # HA CT2 SM SM
+ 2441 13 863 862 860 866 # C CT1 CT2 HA
+ 2442 192 864 862 865 80 # HA CT2 SM SM
+ 2443 13 864 862 860 866 # C CT1 CT2 HA
+ 2444 15 865 862 860 866 # C CT1 CT2 SM
+ 2445 20 866 868 870 873 # C CT2 NH1 C
+ 2446 33 866 868 870 871 # C NH1 CT2 HB
+ 2447 33 866 868 870 872 # C NH1 CT2 HB
+ 2448 164 867 866 868 869 # H NH1 C O
+ 2449 145 867 866 868 870 # CT2 NH1 C O
+ 2450 225 868 870 873 875 # NH1 C CT2 NH1
+ 2451 231 868 870 873 874 # NH1 CT2 C O
+ 2452 21 869 868 870 873 # C CT2 NH1 H
+ 2453 166 869 868 870 871 # H NH1 CT2 HB
+ 2454 166 869 868 870 872 # H NH1 CT2 HB
+ 2455 119 870 873 875 876 # CT2 C NH1 H
+ 2456 117 870 873 875 877 # CT2 C NH1 CT2
+ 2457 118 870 873 875 877 # CT2 C NH1 CT2
+ 2458 211 871 870 873 875 # HB CT2 C NH1
+ 2459 212 871 870 873 874 # HB CT2 C O
+ 2460 211 872 870 873 875 # HB CT2 C NH1
+ 2461 212 872 870 873 874 # HB CT2 C O
+ 2462 20 873 875 877 880 # C CT2 NH1 C
+ 2463 33 873 875 877 878 # C NH1 CT2 HB
+ 2464 33 873 875 877 879 # C NH1 CT2 HB
+ 2465 164 874 873 875 876 # H NH1 C O
+ 2466 145 874 873 875 877 # CT2 NH1 C O
+ 2467 225 875 877 880 882 # NH1 C CT2 NH1
+ 2468 231 875 877 880 881 # NH1 CT2 C O
+ 2469 21 876 875 877 880 # C CT2 NH1 H
+ 2470 166 876 875 877 878 # H NH1 CT2 HB
+ 2471 166 876 875 877 879 # H NH1 CT2 HB
+ 2472 119 877 880 882 883 # CT2 C NH1 H
+ 2473 114 877 880 882 884 # CT1 NH1 C CT2
+ 2474 115 877 880 882 884 # CT1 NH1 C CT2
+ 2475 211 878 877 880 882 # HB CT2 C NH1
+ 2476 212 878 877 880 881 # HB CT2 C O
+ 2477 211 879 877 880 882 # HB CT2 C NH1
+ 2478 212 879 877 880 881 # HB CT2 C O
+ 2479 31 880 882 884 886 # C NH1 CT1 CT3
+ 2480 28 880 882 884 890 # C NH1 CT1 CC
+ 2481 32 880 882 884 885 # C NH1 CT1 HB
+ 2482 164 881 880 882 883 # H NH1 C O
+ 2483 116 881 880 882 884 # CT1 NH1 C O
+ 2484 194 882 884 886 887 # HA CT3 CT1 NH1
+ 2485 194 882 884 886 888 # HA CT3 CT1 NH1
+ 2486 194 882 884 886 889 # HA CT3 CT1 NH1
+ 2487 227 882 884 890 892 # NH1 CT1 CC OC
+ 2488 227 882 884 890 891 # NH1 CT1 CC OC
+ 2489 158 883 882 884 886 # CT3 CT1 NH1 H
+ 2490 44 883 882 884 890 # CC CT1 NH1 H
+ 2491 165 883 882 884 885 # H NH1 CT1 HB
+ 2492 193 885 884 886 887 # HA CT3 CT1 HB
+ 2493 193 885 884 886 888 # HA CT3 CT1 HB
+ 2494 193 885 884 886 889 # HA CT3 CT1 HB
+ 2495 205 885 884 890 892 # HB CT1 CC OC
+ 2496 205 885 884 890 891 # HB CT1 CC OC
+ 2497 152 886 884 890 892 # CT3 CT1 CC OC
+ 2498 152 886 884 890 891 # CT3 CT1 CC OC
+ 2499 43 887 886 884 890 # CC CT1 CT3 HA
+ 2500 43 888 886 884 890 # CC CT1 CT3 HA
+ 2501 43 889 886 884 890 # CC CT1 CT3 HA
+
+Improper Coeffs
+
+ 1 120 0 # C CP1 N O
+ 2 120 0 # C CP1 NH1 O
+ 3 120 0 # C CT1 N O
+ 4 120 0 # C CT1 NH1 O
+ 5 120 0 # C CT2 N O
+ 6 120 0 # C CT2 NH1 O
+ 7 40 0 # C NC2 NC2 NC2
+ 8 96 0 # CC CT1 OC OC
+ 9 45 0 # CC CT2 NH2 O
+ 10 96 0 # CC CT2 OC OC
+ 11 45 0 # CC NH2 CT2 O
+ 12 0 0 # CP3 CP1 C N
+ 13 20 0 # H CT1 C NH1
+ 14 20 0 # H CT2 C NH1
+ 15 4 0 # H H CC NH2
+
+Impropers
+
+ 1 7 18 19 22 16 # C NC2 NC2 NC2
+ 2 3 25 5 27 26 # C CT1 N O
+ 3 2 39 31 41 40 # C CP1 NH1 O
+ 4 13 41 39 43 42 # H CT1 C NH1
+ 5 10 48 45 50 49 # CC CT2 OC OC
+ 6 4 51 43 53 52 # C CT1 NH1 O
+ 7 13 53 51 55 54 # H CT1 C NH1
+ 8 4 71 55 73 72 # C CT1 NH1 O
+ 9 13 73 71 75 74 # H CT1 C NH1
+ 10 4 81 75 83 82 # C CT1 NH1 O
+ 11 13 83 81 85 84 # H CT1 C NH1
+ 12 4 100 85 102 101 # C CT1 NH1 O
+ 13 13 102 100 104 103 # H CT1 C NH1
+ 14 10 112 109 114 113 # CC CT2 OC OC
+ 15 3 115 104 117 116 # C CT1 N O
+ 16 1 129 121 131 130 # C CP1 N O
+ 17 2 143 135 145 144 # C CP1 NH1 O
+ 18 13 145 143 147 146 # H CT1 C NH1
+ 19 4 164 147 166 165 # C CT1 NH1 O
+ 20 13 166 164 168 167 # H CT1 C NH1
+ 21 4 178 168 180 179 # C CT1 NH1 O
+ 22 14 180 178 182 181 # H CT2 C NH1
+ 23 5 185 182 187 186 # C CT2 N O
+ 24 2 199 191 201 200 # C CP1 NH1 O
+ 25 13 201 199 203 202 # H CT1 C NH1
+ 26 4 209 203 211 210 # C CT1 NH1 O
+ 27 13 211 209 213 212 # H CT1 C NH1
+ 28 4 231 213 233 232 # C CT1 NH1 O
+ 29 13 233 231 235 234 # H CT1 C NH1
+ 30 4 241 235 243 242 # C CT1 NH1 O
+ 31 13 243 241 245 244 # H CT1 C NH1
+ 32 7 258 259 262 256 # C NC2 NC2 NC2
+ 33 4 265 245 267 266 # C CT1 NH1 O
+ 34 13 267 265 269 268 # H CT1 C NH1
+ 35 4 284 269 286 285 # C CT1 NH1 O
+ 36 13 286 284 288 287 # H CT1 C NH1
+ 37 4 303 288 305 304 # C CT1 NH1 O
+ 38 13 305 303 307 306 # H CT1 C NH1
+ 39 7 320 321 324 318 # C NC2 NC2 NC2
+ 40 4 327 307 329 328 # C CT1 NH1 O
+ 41 13 329 327 331 330 # H CT1 C NH1
+ 42 4 348 331 350 349 # C CT1 NH1 O
+ 43 13 350 348 352 351 # H CT1 C NH1
+ 44 4 368 352 370 369 # C CT1 NH1 O
+ 45 13 370 368 372 371 # H CT1 C NH1
+ 46 4 389 372 391 390 # C CT1 NH1 O
+ 47 13 391 389 393 392 # H CT1 C NH1
+ 48 11 398 400 395 399 # CC NH2 CT2 O
+ 49 9 398 395 400 399 # CC CT2 NH2 O
+ 50 15 400 398 401 402 # H H CC NH2
+ 51 15 400 398 402 401 # H H CC NH2
+ 52 4 403 393 405 404 # C CT1 NH1 O
+ 53 13 405 403 407 406 # H CT1 C NH1
+ 54 4 413 407 415 414 # C CT1 NH1 O
+ 55 13 415 413 417 416 # H CT1 C NH1
+ 56 4 435 417 437 436 # C CT1 NH1 O
+ 57 13 437 435 439 438 # H CT1 C NH1
+ 58 4 445 439 447 446 # C CT1 NH1 O
+ 59 14 447 445 449 448 # H CT2 C NH1
+ 60 6 452 449 454 453 # C CT2 NH1 O
+ 61 13 454 452 456 455 # H CT1 C NH1
+ 62 4 471 456 473 472 # C CT1 NH1 O
+ 63 13 473 471 475 474 # H CT1 C NH1
+ 64 4 481 475 483 482 # C CT1 NH1 O
+ 65 13 483 481 485 484 # H CT1 C NH1
+ 66 11 493 495 490 494 # CC NH2 CT2 O
+ 67 9 493 490 495 494 # CC CT2 NH2 O
+ 68 15 495 493 496 497 # H H CC NH2
+ 69 15 495 493 497 496 # H H CC NH2
+ 70 4 498 485 500 499 # C CT1 NH1 O
+ 71 13 500 498 502 501 # H CT1 C NH1
+ 72 4 512 502 514 513 # C CT1 NH1 O
+ 73 13 514 512 516 515 # H CT1 C NH1
+ 74 4 532 516 534 533 # C CT1 NH1 O
+ 75 13 534 532 536 535 # H CT1 C NH1
+ 76 4 548 536 550 549 # C CT1 NH1 O
+ 77 13 550 548 552 551 # H CT1 C NH1
+ 78 4 569 552 571 570 # C CT1 NH1 O
+ 79 14 571 569 573 572 # H CT2 C NH1
+ 80 6 576 573 578 577 # C CT2 NH1 O
+ 81 14 578 576 580 579 # H CT2 C NH1
+ 82 6 583 580 585 584 # C CT2 NH1 O
+ 83 13 585 583 587 586 # H CT1 C NH1
+ 84 4 593 587 595 594 # C CT1 NH1 O
+ 85 13 595 593 597 596 # H CT1 C NH1
+ 86 7 610 611 614 608 # C NC2 NC2 NC2
+ 87 4 617 597 619 618 # C CT1 NH1 O
+ 88 13 619 617 621 620 # H CT1 C NH1
+ 89 4 627 621 629 628 # C CT1 NH1 O
+ 90 13 629 627 631 630 # H CT1 C NH1
+ 91 4 649 631 651 650 # C CT1 NH1 O
+ 92 13 651 649 653 652 # H CT1 C NH1
+ 93 7 666 667 670 664 # C NC2 NC2 NC2
+ 94 4 673 653 675 674 # C CT1 NH1 O
+ 95 13 675 673 677 676 # H CT1 C NH1
+ 96 11 682 684 679 683 # CC NH2 CT2 O
+ 97 9 682 679 684 683 # CC CT2 NH2 O
+ 98 15 684 682 685 686 # H H CC NH2
+ 99 15 684 682 686 685 # H H CC NH2
+ 100 4 687 677 689 688 # C CT1 NH1 O
+ 101 13 689 687 691 690 # H CT1 C NH1
+ 102 11 696 698 693 697 # CC NH2 CT2 O
+ 103 9 696 693 698 697 # CC CT2 NH2 O
+ 104 15 698 696 699 700 # H H CC NH2
+ 105 15 698 696 700 699 # H H CC NH2
+ 106 4 701 691 703 702 # C CT1 NH1 O
+ 107 13 703 701 705 704 # H CT1 C NH1
+ 108 4 721 705 723 722 # C CT1 NH1 O
+ 109 13 723 721 725 724 # H CT1 C NH1
+ 110 4 743 725 745 744 # C CT1 NH1 O
+ 111 13 745 743 747 746 # H CT1 C NH1
+ 112 4 754 747 756 755 # C CT1 NH1 O
+ 113 13 756 754 758 757 # H CT1 C NH1
+ 114 4 764 758 766 765 # C CT1 NH1 O
+ 115 13 766 764 768 767 # H CT1 C NH1
+ 116 10 776 773 778 777 # CC CT2 OC OC
+ 117 4 779 768 781 780 # C CT1 NH1 O
+ 118 13 781 779 783 782 # H CT1 C NH1
+ 119 10 788 785 790 789 # CC CT2 OC OC
+ 120 4 791 783 793 792 # C CT1 NH1 O
+ 121 13 793 791 795 794 # H CT1 C NH1
+ 122 4 801 795 803 802 # C CT1 NH1 O
+ 123 13 803 801 805 804 # H CT1 C NH1
+ 124 4 818 805 820 819 # C CT1 NH1 O
+ 125 13 820 818 822 821 # H CT1 C NH1
+ 126 7 835 836 839 833 # C NC2 NC2 NC2
+ 127 4 842 822 844 843 # C CT1 NH1 O
+ 128 13 844 842 846 845 # H CT1 C NH1
+ 129 4 856 846 858 857 # C CT1 NH1 O
+ 130 13 858 856 860 859 # H CT1 C NH1
+ 131 4 866 860 868 867 # C CT1 NH1 O
+ 132 14 868 866 870 869 # H CT2 C NH1
+ 133 6 873 870 875 874 # C CT2 NH1 O
+ 134 14 875 873 877 876 # H CT2 C NH1
+ 135 6 880 877 882 881 # C CT2 NH1 O
+ 136 13 882 880 884 883 # H CT1 C NH1
+ 137 8 890 884 892 891 # CC CT1 OC OC
+
diff --git a/examples/USER/misc/filter-corotate/data.peptide b/examples/USER/misc/filter-corotate/data.peptide
new file mode 100644
index 0000000000000000000000000000000000000000..f9dfb6e485302da2abd338eb1be299011f4aeba7
--- /dev/null
+++ b/examples/USER/misc/filter-corotate/data.peptide
@@ -0,0 +1,6531 @@
+LAMMPS Description
+
+ 2004 atoms
+ 1365 bonds
+ 786 angles
+ 207 dihedrals
+ 12 impropers
+
+ 14 atom types
+ 18 bond types
+ 31 angle types
+ 21 dihedral types
+ 2 improper types
+
+ 36.840194 64.211560 xlo xhi
+ 41.013691 68.385058 ylo yhi
+ 29.768095 57.139462 zlo zhi
+
+Masses
+
+ 1 12.0110
+ 2 12.0110
+ 3 15.9990
+ 4 1.0080
+ 5 14.0070
+ 6 12.0110
+ 7 12.0110
+ 8 12.0110
+ 9 15.9990
+ 10 1.0080
+ 11 1.0080
+ 12 32.0660
+ 13 16.0000
+ 14 1.0100
+
+Pair Coeffs
+
+ 1 0.110000 3.563595 0.110000 3.563595
+ 2 0.080000 3.670503 0.010000 3.385415
+ 3 0.120000 3.029056 0.120000 2.494516
+ 4 0.022000 2.351973 0.022000 2.351973
+ 5 0.200000 3.296325 0.200000 2.761786
+ 6 0.020000 4.053589 0.010000 3.385415
+ 7 0.055000 3.875410 0.010000 3.385415
+ 8 0.070000 3.550053 0.070000 3.550053
+ 9 0.152100 3.153782 0.152100 3.153782
+ 10 0.046000 0.400014 0.046000 0.400014
+ 11 0.030000 2.420037 0.030000 2.420037
+ 12 0.450000 3.563595 0.450000 3.563595
+ 13 0.152100 3.150570 0.152100 3.150570
+ 14 0.046000 0.400014 0.046000 0.400014
+
+Bond Coeffs
+
+ 1 249.999999 1.490000
+ 2 620.000001 1.230000
+ 3 370.000000 1.345000
+ 4 322.000001 1.111000
+ 5 319.999999 1.430000
+ 6 440.000000 0.997000
+ 7 222.500001 1.538000
+ 8 330.000001 1.080000
+ 9 230.000000 1.490000
+ 10 309.000001 1.111000
+ 11 305.000000 1.375000
+ 12 340.000001 1.080000
+ 13 334.300000 1.411000
+ 14 545.000001 0.960000
+ 15 222.500001 1.530000
+ 16 198.000000 1.818000
+ 17 239.999999 1.816000
+ 18 450.000000 0.957200
+
+Angle Coeffs
+
+ 1 33.000000 109.500000 30.000000 2.163000
+ 2 50.000000 120.000000 0.000000 0.000000
+ 3 34.000000 123.000000 0.000000 0.000000
+ 4 80.000000 121.000000 0.000000 0.000000
+ 5 80.000000 116.500000 0.000000 0.000000
+ 6 80.000000 122.500000 0.000000 0.000000
+ 7 35.500000 108.400000 5.400000 1.802000
+ 8 50.000000 107.000000 0.000000 0.000000
+ 9 70.000000 113.500000 0.000000 0.000000
+ 10 48.000000 108.000000 0.000000 0.000000
+ 11 35.000000 117.000000 0.000000 0.000000
+ 12 51.800000 107.500000 0.000000 0.000000
+ 13 33.430000 110.100000 22.530000 2.179000
+ 14 52.000000 108.000000 0.000000 0.000000
+ 15 50.000000 109.500000 0.000000 0.000000
+ 16 35.000000 111.000000 0.000000 0.000000
+ 17 45.800000 122.300000 0.000000 0.000000
+ 18 49.300000 107.500000 0.000000 0.000000
+ 19 40.000000 120.000000 35.000000 2.416200
+ 20 30.000000 120.000000 22.000000 2.152500
+ 21 45.200000 120.000000 0.000000 0.000000
+ 22 65.000000 108.000000 0.000000 0.000000
+ 23 35.500000 109.000000 5.400000 1.802000
+ 24 36.000000 115.000000 0.000000 0.000000
+ 25 58.350000 113.500000 11.160000 2.561000
+ 26 58.000000 114.500000 0.000000 0.000000
+ 27 26.500000 110.100000 22.530000 2.179000
+ 28 34.000000 95.000000 0.000000 0.000000
+ 29 46.100000 111.300000 0.000000 0.000000
+ 30 51.500000 109.500000 0.000000 0.000000
+ 31 55.000000 104.520000 0.000000 0.000000
+
+Dihedral Coeffs
+
+ 1 0.200000 1 180 1.000000
+ 2 1.800000 1 0 1.000000
+ 3 0.000000 1 0 1.000000
+ 4 1.600000 1 0 0.500000
+ 5 2.500000 2 180 0.500000
+ 6 2.500000 2 180 1.000000
+ 7 0.600000 1 0 1.000000
+ 8 0.200000 3 0 1.000000
+ 9 0.230000 2 180 1.000000
+ 10 0.040000 3 0 1.000000
+ 11 1.400000 1 0 1.000000
+ 12 3.100000 2 180 1.000000
+ 13 4.200000 2 180 1.000000
+ 14 3.100000 2 180 0.500000
+ 15 0.990000 2 180 1.000000
+ 16 2.400000 2 180 1.000000
+ 17 0.195000 3 0 1.000000
+ 18 0.240000 1 180 0.500000
+ 19 0.370000 3 0 0.500000
+ 20 0.280000 3 0 1.000000
+ 21 0.010000 3 0 1.000000
+
+Improper Coeffs
+
+ 1 120.000000 0.000000
+ 2 20.000000 0.000000
+
+Atoms
+
+ 1 1 1 0.510 43.99993 58.52678 36.78550 0 0 0
+ 2 1 2 -0.270 45.10395 58.23499 35.86693 0 0 0
+ 3 1 3 -0.510 43.81519 59.54928 37.43995 0 0 0
+ 4 1 4 0.090 45.71714 57.34797 36.13434 0 0 0
+ 5 1 4 0.090 45.72261 59.13657 35.67007 0 0 0
+ 6 1 4 0.090 44.66624 58.09539 34.85538 0 0 0
+ 7 1 5 -0.470 43.28193 57.47427 36.91953 0 0 0
+ 8 1 6 0.070 42.07157 57.45486 37.62418 0 0 0
+ 9 1 1 0.510 42.19985 57.57789 39.12163 0 0 0
+ 10 1 3 -0.510 41.88641 58.62251 39.70398 0 0 0
+ 11 1 7 -0.180 41.25052 56.15304 37.41811 0 0 0
+ 12 1 8 0.000 40.88511 55.94638 35.97460 0 0 0
+ 13 1 8 -0.115 41.48305 54.96372 35.11223 0 0 0
+ 14 1 8 -0.115 39.74003 56.60996 35.46443 0 0 0
+ 15 1 8 -0.115 41.02111 54.75715 33.80764 0 0 0
+ 16 1 8 -0.115 39.26180 56.39194 34.12024 0 0 0
+ 17 1 8 0.110 39.92330 55.46092 33.27135 0 0 0
+ 18 1 9 -0.540 39.48164 55.22919 31.91865 0 0 0
+ 19 1 10 0.310 43.60633 56.61693 36.52744 0 0 0
+ 20 1 4 0.090 41.49619 58.31145 37.30543 0 0 0
+ 21 1 4 0.090 41.88498 55.29476 37.72657 0 0 0
+ 22 1 4 0.090 40.30899 56.19690 38.00627 0 0 0
+ 23 1 11 0.115 42.31528 54.36176 35.44606 0 0 0
+ 24 1 11 0.115 39.26330 57.31216 36.13230 0 0 0
+ 25 1 11 0.115 41.62695 54.10606 33.19490 0 0 0
+ 26 1 11 0.115 38.42147 56.98236 33.78612 0 0 0
+ 27 1 10 0.430 38.78233 55.86217 31.74004 0 0 0
+ 28 1 5 -0.470 42.79933 56.56370 39.79000 0 0 0
+ 29 1 7 -0.020 42.96709 56.75379 41.28116 0 0 0
+ 30 1 1 0.510 43.83019 55.68988 41.92255 0 0 0
+ 31 1 3 -0.510 44.98521 55.93104 42.21713 0 0 0
+ 32 1 10 0.310 43.13466 55.75696 39.30966 0 0 0
+ 33 1 4 0.090 42.04692 56.86721 41.83507 0 0 0
+ 34 1 4 0.090 43.52938 57.66324 41.43329 0 0 0
+ 35 1 5 -0.470 43.26792 54.43342 42.07043 0 0 0
+ 36 1 7 -0.020 43.92411 53.28930 42.63327 0 0 0
+ 37 1 1 0.510 43.51012 53.02289 44.10510 0 0 0
+ 38 1 3 -0.510 42.35086 53.07863 44.50806 0 0 0
+ 39 1 10 0.310 42.28859 54.34993 41.90323 0 0 0
+ 40 1 4 0.090 44.98464 53.47473 42.54797 0 0 0
+ 41 1 4 0.090 43.49715 52.54787 41.97419 0 0 0
+ 42 1 5 -0.470 44.51925 52.64535 44.88133 0 0 0
+ 43 1 6 0.070 44.47588 52.35054 46.24397 0 0 0
+ 44 1 1 0.510 45.40218 53.34579 46.94730 0 0 0
+ 45 1 3 -0.510 45.23520 54.55893 46.92038 0 0 0
+ 46 1 7 -0.180 44.77960 50.82831 46.50232 0 0 0
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+
+Dihedrals
+
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+ 29 8 20 8 11 21
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+ 207 3 64 79 80 82
+
+Impropers
+
+ 1 2 7 1 8 19
+ 2 1 1 2 7 3
+ 3 1 9 8 28 10
+ 4 2 28 9 29 32
+ 5 1 30 29 35 31
+ 6 2 35 30 36 39
+ 7 1 37 36 42 38
+ 8 2 42 37 43 53
+ 9 1 44 43 62 45
+ 10 2 62 44 63 70
+ 11 1 64 63 79 65
+ 12 2 79 64 80 81
diff --git a/examples/USER/misc/filter-corotate/in.bpti b/examples/USER/misc/filter-corotate/in.bpti
new file mode 100644
index 0000000000000000000000000000000000000000..6507a78704700a7b9ffa754103b279bf6c886ce3
--- /dev/null
+++ b/examples/USER/misc/filter-corotate/in.bpti
@@ -0,0 +1,43 @@
+
+units real
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+
+pair_style lj/charmm/coul/long 8 10
+pair_modify mix arithmetic
+kspace_style pppm 1e-4
+
+read_data data.bpti
+
+special_bonds charmm
+neigh_modify delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 1e-4 1e-6 1000 10000
+reset_timestep 0
+
+# ------------- RUN ---------------
+
+thermo 100
+thermo_style multi
+timestep 8
+
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+
+velocity all create 200.0 12345678 dist uniform
+#dump dump1 all atom 100 4pti.dump
+
+fix 1 all nvt temp 200 300 25
+fix cor all filter/corotate m 1.0
+
+run 1000
+
+unfix cor
+unfix 1
+
diff --git a/examples/USER/misc/filter-corotate/in.peptide b/examples/USER/misc/filter-corotate/in.peptide
new file mode 100644
index 0000000000000000000000000000000000000000..0a17f995b3c58324d190cb46072ca3a0c54633b3
--- /dev/null
+++ b/examples/USER/misc/filter-corotate/in.peptide
@@ -0,0 +1,32 @@
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units real
+atom_style full
+
+pair_style lj/charmm/coul/long 8.0 10.0 10.0
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+kspace_style pppm 0.0001
+
+read_data data.peptide
+
+neighbor 2.0 bin
+neigh_modify delay 5
+
+thermo 50
+#dump dump1 all atom 100 peptide.dump
+
+timestep 8
+
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+
+fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix cor all filter/corotate m 1.0
+run 1000
+unfix cor
+unfix 1
+
+
+
diff --git a/examples/USER/misc/filter-corotate/log.10Mar2017.bpti.g++.1 b/examples/USER/misc/filter-corotate/log.10Mar2017.bpti.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..5253b47b2da56967e3950869f253c1b8939a50c8
--- /dev/null
+++ b/examples/USER/misc/filter-corotate/log.10Mar2017.bpti.g++.1
@@ -0,0 +1,240 @@
+LAMMPS (10 Mar 2017)
+ using 1 OpenMP thread(s) per MPI task
+
+units real
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+
+pair_style lj/charmm/coul/long 8 10
+pair_modify mix arithmetic
+kspace_style pppm 1e-4
+
+read_data data.bpti
+ orthogonal box = (-10 -10 -30) to (50 50 30)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 892 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 18 = max dihedrals/atom
+ scanning impropers ...
+ 2 = max impropers/atom
+ reading bonds ...
+ 906 bonds
+ reading angles ...
+ 1626 angles
+ reading dihedrals ...
+ 2501 dihedrals
+ reading impropers ...
+ 137 impropers
+ 4 = max # of 1-2 neighbors
+ 9 = max # of 1-3 neighbors
+ 19 = max # of 1-4 neighbors
+ 21 = max # of special neighbors
+
+special_bonds charmm
+neigh_modify delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 1e-4 1e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.203272
+ grid = 16 16 16
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0316399
+ estimated relative force accuracy = 9.52826e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 9261 4096
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/charmm/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -3075.6498 943.91164 -2131.7381 -380.67776
+ 241 0 -4503.313 749.58662 -3753.7264 -29.045104
+Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms
+
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -2131.73812515 -3753.43984087 -3753.72636847
+ Force two-norm initial, final = 1086.21 26.3688
+ Force max component initial, final = 310.811 3.92748
+ Final line search alpha, max atom move = 0.00596649 0.0234333
+ Iterations, force evaluations = 241 463
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.5003 | 2.5003 | 2.5003 | 0.0 | 74.48
+Bond | 0.24287 | 0.24287 | 0.24287 | 0.0 | 7.23
+Kspace | 0.53428 | 0.53428 | 0.53428 | 0.0 | 15.91
+Neigh | 0.069765 | 0.069765 | 0.069765 | 0.0 | 2.08
+Comm | 0.00065374 | 0.00065374 | 0.00065374 | 0.0 | 0.02
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.009358 | | | 0.28
+
+Nlocal: 892 ave 892 max 892 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 31 ave 31 max 31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 148891 ave 148891 max 148891 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 148891
+Ave neighs/atom = 166.918
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 15
+Dangerous builds = 0
+reset_timestep 0
+
+# ------------- RUN ---------------
+
+thermo 100
+thermo_style multi
+timestep 8
+
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+Respa levels:
+ 1 = bond angle dihedral improper
+ 2 = pair
+ 3 = kspace
+
+velocity all create 200.0 12345678 dist uniform
+#dump dump1 all atom 100 4pti.dump
+
+fix 1 all nvt temp 200 300 25
+fix cor all filter/corotate m 1.0
+ 163 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 25 = # of size 4 clusters
+ 0 = # of size 5 clusters
+ 100 = # of frozen angles
+
+run 1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.203272
+ grid = 16 16 16
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0316399
+ estimated relative force accuracy = 9.52826e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 9261 4096
+Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
+PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592
+E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
+E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283
+---------------- Step 100 ----- CPU = 3.9414 (sec) ----------------
+TotEng = -2718.8970 KinEng = 538.6206 Temp = 202.8014
+PotEng = -3257.5176 E_bond = 203.3367 E_angle = 566.5317
+E_dihed = 397.6202 E_impro = 34.6623 E_vdwl = -248.7451
+E_coul = -874.5122 E_long = -3336.4111 Press = 135.8662
+---------------- Step 200 ----- CPU = 7.9028 (sec) ----------------
+TotEng = -2660.1406 KinEng = 626.3319 Temp = 235.8265
+PotEng = -3286.4725 E_bond = 209.5147 E_angle = 591.7773
+E_dihed = 388.9591 E_impro = 29.4992 E_vdwl = -243.5808
+E_coul = -923.5115 E_long = -3339.1306 Press = 88.9000
+---------------- Step 300 ----- CPU = 11.8246 (sec) ----------------
+TotEng = -2673.8090 KinEng = 616.7924 Temp = 232.2346
+PotEng = -3290.6014 E_bond = 202.8254 E_angle = 568.6860
+E_dihed = 378.4182 E_impro = 38.2399 E_vdwl = -221.3236
+E_coul = -915.3004 E_long = -3342.1468 Press = 78.8527
+---------------- Step 400 ----- CPU = 15.7990 (sec) ----------------
+TotEng = -2614.9416 KinEng = 649.3474 Temp = 244.4922
+PotEng = -3264.2890 E_bond = 211.6116 E_angle = 617.2026
+E_dihed = 399.8744 E_impro = 40.2678 E_vdwl = -211.7790
+E_coul = -978.1624 E_long = -3343.3041 Press = -4.1958
+---------------- Step 500 ----- CPU = 19.8146 (sec) ----------------
+TotEng = -2588.6772 KinEng = 660.1424 Temp = 248.5568
+PotEng = -3248.8196 E_bond = 218.4786 E_angle = 620.8605
+E_dihed = 390.3220 E_impro = 41.6794 E_vdwl = -226.3657
+E_coul = -953.1676 E_long = -3340.6269 Press = 99.3200
+---------------- Step 600 ----- CPU = 23.8587 (sec) ----------------
+TotEng = -2550.4618 KinEng = 693.3384 Temp = 261.0557
+PotEng = -3243.8002 E_bond = 232.3563 E_angle = 606.2922
+E_dihed = 396.2469 E_impro = 37.1980 E_vdwl = -235.8425
+E_coul = -937.1208 E_long = -3342.9303 Press = -21.7737
+---------------- Step 700 ----- CPU = 27.8381 (sec) ----------------
+TotEng = -2554.4355 KinEng = 692.8951 Temp = 260.8888
+PotEng = -3247.3306 E_bond = 216.3395 E_angle = 637.7785
+E_dihed = 391.5940 E_impro = 43.1426 E_vdwl = -187.6159
+E_coul = -1008.1694 E_long = -3340.3998 Press = 75.1484
+---------------- Step 800 ----- CPU = 31.8039 (sec) ----------------
+TotEng = -2508.3551 KinEng = 699.0766 Temp = 263.2163
+PotEng = -3207.4317 E_bond = 241.9936 E_angle = 641.3631
+E_dihed = 386.2198 E_impro = 43.7793 E_vdwl = -217.7523
+E_coul = -964.6070 E_long = -3338.4282 Press = -127.7337
+---------------- Step 900 ----- CPU = 35.7700 (sec) ----------------
+TotEng = -2452.7644 KinEng = 762.1842 Temp = 286.9776
+PotEng = -3214.9485 E_bond = 243.9191 E_angle = 649.8664
+E_dihed = 382.4351 E_impro = 39.0029 E_vdwl = -221.3389
+E_coul = -970.8965 E_long = -3337.9366 Press = 122.7720
+---------------- Step 1000 ----- CPU = 39.7695 (sec) ----------------
+TotEng = -2386.6805 KinEng = 799.0253 Temp = 300.8490
+PotEng = -3185.7058 E_bond = 265.3649 E_angle = 661.7543
+E_dihed = 374.6843 E_impro = 38.6877 E_vdwl = -229.2030
+E_coul = -960.7041 E_long = -3336.2899 Press = -17.9910
+Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms
+
+Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 29.169 | 29.169 | 29.169 | 0.0 | 73.34
+Bond | 7.6249 | 7.6249 | 7.6249 | 0.0 | 19.17
+Kspace | 1.1525 | 1.1525 | 1.1525 | 0.0 | 2.90
+Neigh | 0.87606 | 0.87606 | 0.87606 | 0.0 | 2.20
+Comm | 0.01563 | 0.01563 | 0.01563 | 0.0 | 0.04
+Output | 0.00048423 | 0.00048423 | 0.00048423 | 0.0 | 0.00
+Modify | 0.80446 | 0.80446 | 0.80446 | 0.0 | 2.02
+Other | | 0.1266 | | | 0.32
+
+Nlocal: 892 ave 892 max 892 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 27 ave 27 max 27 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 146206 ave 146206 max 146206 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 146206
+Ave neighs/atom = 163.908
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 186
+Dangerous builds = 0
+
+unfix cor
+unfix 1
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:43
diff --git a/examples/USER/misc/filter-corotate/log.10Mar2017.bpti.g++.4 b/examples/USER/misc/filter-corotate/log.10Mar2017.bpti.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..4300c1caf50be1ac16de30c251d27a31c41e3e1e
--- /dev/null
+++ b/examples/USER/misc/filter-corotate/log.10Mar2017.bpti.g++.4
@@ -0,0 +1,240 @@
+LAMMPS (10 Mar 2017)
+ using 1 OpenMP thread(s) per MPI task
+
+units real
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+
+pair_style lj/charmm/coul/long 8 10
+pair_modify mix arithmetic
+kspace_style pppm 1e-4
+
+read_data data.bpti
+ orthogonal box = (-10 -10 -30) to (50 50 30)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 892 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 18 = max dihedrals/atom
+ scanning impropers ...
+ 2 = max impropers/atom
+ reading bonds ...
+ 906 bonds
+ reading angles ...
+ 1626 angles
+ reading dihedrals ...
+ 2501 dihedrals
+ reading impropers ...
+ 137 impropers
+ 4 = max # of 1-2 neighbors
+ 9 = max # of 1-3 neighbors
+ 19 = max # of 1-4 neighbors
+ 21 = max # of special neighbors
+
+special_bonds charmm
+neigh_modify delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 1e-4 1e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.203272
+ grid = 16 16 16
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0316399
+ estimated relative force accuracy = 9.52826e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 3549 1024
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/charmm/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory usage (min/avg/max) = 16.9693/0.981879/0 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -3075.6498 943.91164 -2131.7381 -380.67776
+ 241 0 -4503.3131 749.58666 -3753.7264 -29.045153
+Loop time of 1.26594 on 4 procs for 241 steps with 892 atoms
+
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -2131.73812515 -3753.43983927 -3753.72640137
+ Force two-norm initial, final = 1086.21 26.3688
+ Force max component initial, final = 310.811 3.92751
+ Final line search alpha, max atom move = 0.00596649 0.0234334
+ Iterations, force evaluations = 241 463
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.34267 | 0.63792 | 0.90268 | 25.2 | 50.39
+Bond | 0.025776 | 0.063318 | 0.095631 | 10.8 | 5.00
+Kspace | 0.21904 | 0.51601 | 0.84895 | 31.3 | 40.76
+Neigh | 0.023185 | 0.023363 | 0.023538 | 0.1 | 1.85
+Comm | 0.012025 | 0.014189 | 0.016335 | 1.4 | 1.12
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.01114 | | | 0.88
+
+Nlocal: 223 ave 323 max 89 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 613 ave 675 max 557 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs: 37222.8 ave 50005 max 20830 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+
+Total # of neighbors = 148891
+Ave neighs/atom = 166.918
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 15
+Dangerous builds = 0
+reset_timestep 0
+
+# ------------- RUN ---------------
+
+thermo 100
+thermo_style multi
+timestep 8
+
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+Respa levels:
+ 1 = bond angle dihedral improper
+ 2 = pair
+ 3 = kspace
+
+velocity all create 200.0 12345678 dist uniform
+#dump dump1 all atom 100 4pti.dump
+
+fix 1 all nvt temp 200 300 25
+fix cor all filter/corotate m 1.0
+ 163 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 25 = # of size 4 clusters
+ 0 = # of size 5 clusters
+ 100 = # of frozen angles
+
+run 1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.203272
+ grid = 16 16 16
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0316399
+ estimated relative force accuracy = 9.52826e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 3549 1024
+Per MPI rank memory usage (min/avg/max) = 17.142/0.97212/0 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
+PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2592
+E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
+E_coul = -886.3622 E_long = -3326.2088 Press = 83.2282
+---------------- Step 100 ----- CPU = 1.5457 (sec) ----------------
+TotEng = -2718.9184 KinEng = 538.6205 Temp = 202.8014
+PotEng = -3257.5389 E_bond = 203.3365 E_angle = 566.5311
+E_dihed = 397.6202 E_impro = 34.6621 E_vdwl = -248.7451
+E_coul = -874.5326 E_long = -3336.4111 Press = 135.8435
+---------------- Step 200 ----- CPU = 3.0720 (sec) ----------------
+TotEng = -2660.1146 KinEng = 626.3474 Temp = 235.8323
+PotEng = -3286.4620 E_bond = 209.5168 E_angle = 591.7735
+E_dihed = 388.9615 E_impro = 29.5000 E_vdwl = -243.5840
+E_coul = -923.4998 E_long = -3339.1299 Press = 88.8857
+---------------- Step 300 ----- CPU = 4.5597 (sec) ----------------
+TotEng = -2669.7442 KinEng = 619.3625 Temp = 233.2023
+PotEng = -3289.1067 E_bond = 203.4405 E_angle = 569.5281
+E_dihed = 378.3314 E_impro = 38.2880 E_vdwl = -221.1904
+E_coul = -915.3396 E_long = -3342.1646 Press = 79.3780
+---------------- Step 400 ----- CPU = 5.9808 (sec) ----------------
+TotEng = -2618.9975 KinEng = 644.6145 Temp = 242.7102
+PotEng = -3263.6119 E_bond = 209.5864 E_angle = 618.8954
+E_dihed = 401.3798 E_impro = 39.9064 E_vdwl = -212.1271
+E_coul = -977.1589 E_long = -3344.0940 Press = -7.8938
+---------------- Step 500 ----- CPU = 7.4159 (sec) ----------------
+TotEng = -2579.7486 KinEng = 666.4643 Temp = 250.9371
+PotEng = -3246.2129 E_bond = 219.2549 E_angle = 620.3474
+E_dihed = 388.4395 E_impro = 41.4499 E_vdwl = -225.9686
+E_coul = -949.3689 E_long = -3340.3672 Press = 113.2543
+---------------- Step 600 ----- CPU = 8.9252 (sec) ----------------
+TotEng = -2535.8235 KinEng = 708.5919 Temp = 266.7990
+PotEng = -3244.4154 E_bond = 243.9451 E_angle = 606.0866
+E_dihed = 400.0562 E_impro = 33.9708 E_vdwl = -223.1319
+E_coul = -964.9940 E_long = -3340.3482 Press = -102.4475
+---------------- Step 700 ----- CPU = 10.4022 (sec) ----------------
+TotEng = -2552.6681 KinEng = 702.3080 Temp = 264.4330
+PotEng = -3254.9761 E_bond = 250.8834 E_angle = 639.0977
+E_dihed = 386.4014 E_impro = 42.3004 E_vdwl = -224.4816
+E_coul = -1011.8551 E_long = -3337.3222 Press = 10.6424
+---------------- Step 800 ----- CPU = 11.8699 (sec) ----------------
+TotEng = -2423.5415 KinEng = 772.1254 Temp = 290.7206
+PotEng = -3195.6670 E_bond = 238.5831 E_angle = 640.9180
+E_dihed = 377.7994 E_impro = 40.3135 E_vdwl = -216.5705
+E_coul = -935.1087 E_long = -3341.6019 Press = -38.2479
+---------------- Step 900 ----- CPU = 13.3548 (sec) ----------------
+TotEng = -2394.4779 KinEng = 766.6895 Temp = 288.6739
+PotEng = -3161.1673 E_bond = 284.8428 E_angle = 671.0959
+E_dihed = 380.3406 E_impro = 51.2975 E_vdwl = -219.5211
+E_coul = -990.6305 E_long = -3338.5925 Press = -15.2279
+---------------- Step 1000 ----- CPU = 14.7908 (sec) ----------------
+TotEng = -2340.1471 KinEng = 799.0198 Temp = 300.8469
+PotEng = -3139.1669 E_bond = 271.0389 E_angle = 683.8278
+E_dihed = 407.0795 E_impro = 39.6209 E_vdwl = -230.5355
+E_coul = -974.2981 E_long = -3335.9003 Press = -94.3420
+Loop time of 14.7909 on 4 procs for 1000 steps with 892 atoms
+
+Performance: 46.732 ns/day, 0.514 hours/ns, 67.609 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.4184 | 7.5543 | 10.133 | 74.2 | 51.07
+Bond | 0.94027 | 1.9781 | 2.7492 | 54.4 | 13.37
+Kspace | 0.45487 | 0.45887 | 0.46343 | 0.4 | 3.10
+Neigh | 0.28145 | 0.28339 | 0.28539 | 0.3 | 1.92
+Comm | 0.7515 | 4.1484 | 8.3861 | 135.5 | 28.05
+Output | 0.00049973 | 0.00055474 | 0.00066924 | 0.0 | 0.00
+Modify | 0.26165 | 0.31142 | 0.35023 | 6.7 | 2.11
+Other | | 0.05572 | | | 0.38
+
+Nlocal: 223 ave 313 max 122 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost: 584.5 ave 605 max 553 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs: 35448 ave 42093 max 25175 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 141792
+Ave neighs/atom = 158.96
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 186
+Dangerous builds = 0
+
+unfix cor
+unfix 1
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:16
diff --git a/examples/USER/misc/filter-corotate/log.10Mar2017.peptide.g++.1 b/examples/USER/misc/filter-corotate/log.10Mar2017.peptide.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..23dd4c8a89982174b72613ce0a14dde3e0d96bf0
--- /dev/null
+++ b/examples/USER/misc/filter-corotate/log.10Mar2017.peptide.g++.1
@@ -0,0 +1,146 @@
+LAMMPS (10 Mar 2017)
+ using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units real
+atom_style full
+
+pair_style lj/charmm/coul/long 8.0 10.0 10.0
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+kspace_style pppm 0.0001
+
+read_data data.peptide
+ orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 2004 atoms
+ reading velocities ...
+ 2004 velocities
+ scanning bonds ...
+ 3 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 14 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 1365 bonds
+ reading angles ...
+ 786 angles
+ reading dihedrals ...
+ 207 dihedrals
+ reading impropers ...
+ 12 impropers
+ 4 = max # of 1-2 neighbors
+ 7 = max # of 1-3 neighbors
+ 14 = max # of 1-4 neighbors
+ 18 = max # of special neighbors
+
+neighbor 2.0 bin
+neigh_modify delay 5
+
+thermo 50
+#dump dump1 all atom 100 peptide.dump
+
+timestep 8
+
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+Respa levels:
+ 1 = bond angle dihedral improper
+ 2 = pair
+ 3 = kspace
+
+fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix cor all filter/corotate m 1.0
+ 19 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 3 = # of size 4 clusters
+ 0 = # of size 5 clusters
+ 646 = # of frozen angles
+run 1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.268725
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0228209
+ estimated relative force accuracy = 6.87243e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 5 5 5
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/charmm/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
+ 50 239.46028 -7546.5667 1092.8874 -5023.9668 -24643.891
+ 100 242.81799 -7125.5527 416.0788 -5259.7139 15525.465
+ 150 235.97108 -7531.9334 932.35464 -5190.6987 -14838.489
+ 200 252.06415 -7195.6011 568.02993 -5122.6064 8841.332
+ 250 249.99431 -7586.5092 881.83491 -5212.0676 -9330.345
+ 300 240.3382 -7333.0933 633.29951 -5264.8395 5137.9757
+ 350 255.34529 -7568.2413 856.46371 -5187.2226 -6206.063
+ 400 242.99276 -7419.9031 713.23943 -5255.8602 2447.0091
+ 450 251.10653 -7622.061 844.20584 -5278.6079 -4906.6559
+ 500 255.59314 -7439.253 710.84907 -5202.3691 1571.0032
+ 550 253.2025 -7660.5101 823.05373 -5325.695 -4551.399
+ 600 249.05313 -7509.6729 741.48104 -5281.2046 992.87
+ 650 251.75984 -7593.6589 847.08244 -5243.4286 -3510.1176
+ 700 249.25027 -7601.9112 794.0912 -5319.6557 305.76021
+ 750 255.415 -7602.2674 822.98524 -5254.3109 -2333.421
+ 800 241.99621 -7643.8878 796.53352 -5402.5008 -298.66565
+ 850 253.6428 -7598.3764 816.45457 -5267.5316 -1905.3478
+ 900 247.20231 -7690.2806 789.75999 -5424.5838 -1331.7228
+ 950 255.92583 -7634.7505 831.18272 -5275.5466 -2186.5117
+ 1000 253.2126 -7647.9526 823.93602 -5312.195 -1189.9659
+Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms
+
+Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 135.81 | 135.81 | 135.81 | 0.0 | 90.14
+Bond | 2.5889 | 2.5889 | 2.5889 | 0.0 | 1.72
+Kspace | 2.0379 | 2.0379 | 2.0379 | 0.0 | 1.35
+Neigh | 5.893 | 5.893 | 5.893 | 0.0 | 3.91
+Comm | 1.6998 | 1.6998 | 1.6998 | 0.0 | 1.13
+Output | 0.00077915 | 0.00077915 | 0.00077915 | 0.0 | 0.00
+Modify | 2 | 2 | 2 | 0.0 | 1.33
+Other | | 0.6352 | | | 0.42
+
+Nlocal: 2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 11197 ave 11197 max 11197 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 707779 ave 707779 max 707779 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 707779
+Ave neighs/atom = 353.183
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 200
+unfix cor
+unfix 1
+
+
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:02:30
diff --git a/examples/USER/misc/filter-corotate/log.10Mar2017.peptide.g++.4 b/examples/USER/misc/filter-corotate/log.10Mar2017.peptide.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..2cdd645fe3e1b97ef2ae934445e97cad92ad2a7d
--- /dev/null
+++ b/examples/USER/misc/filter-corotate/log.10Mar2017.peptide.g++.4
@@ -0,0 +1,146 @@
+LAMMPS (10 Mar 2017)
+ using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units real
+atom_style full
+
+pair_style lj/charmm/coul/long 8.0 10.0 10.0
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+kspace_style pppm 0.0001
+
+read_data data.peptide
+ orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 2004 atoms
+ reading velocities ...
+ 2004 velocities
+ scanning bonds ...
+ 3 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 14 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 1365 bonds
+ reading angles ...
+ 786 angles
+ reading dihedrals ...
+ 207 dihedrals
+ reading impropers ...
+ 12 impropers
+ 4 = max # of 1-2 neighbors
+ 7 = max # of 1-3 neighbors
+ 14 = max # of 1-4 neighbors
+ 18 = max # of special neighbors
+
+neighbor 2.0 bin
+neigh_modify delay 5
+
+thermo 50
+#dump dump1 all atom 100 peptide.dump
+
+timestep 8
+
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+Respa levels:
+ 1 = bond angle dihedral improper
+ 2 = pair
+ 3 = kspace
+
+fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix cor all filter/corotate m 1.0
+ 19 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 3 = # of size 4 clusters
+ 0 = # of size 5 clusters
+ 646 = # of frozen angles
+run 1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.268725
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0228209
+ estimated relative force accuracy = 6.87243e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 5 5 5
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/charmm/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory usage (min/avg/max) = 16.8394/0.98826/0 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
+ 50 239.46028 -7546.5668 1092.8874 -5023.9668 -24643.891
+ 100 242.81819 -7125.5629 416.08082 -5259.7209 15525.244
+ 150 235.94928 -7531.9186 932.50658 -5190.6621 -14842.431
+ 200 255.85551 -7254.4065 568.8803 -5157.9249 8936.8651
+ 250 247.8705 -7607.4583 858.06087 -5269.4711 -9926.0442
+ 300 257.64176 -7267.424 618.5573 -5110.6004 5173.3307
+ 350 251.65439 -7572.3806 821.15745 -5248.7049 -7092.327
+ 400 256.87927 -7414.2145 655.33178 -5225.169 4119.4095
+ 450 257.12393 -7576.5541 853.39773 -5187.9819 -5224.8823
+ 500 242.42371 -7524.705 705.75357 -5371.5455 2111.3878
+ 550 248.97188 -7541.076 792.86994 -5261.7038 -2278.4185
+ 600 249.81862 -7592.0499 767.17722 -5333.3149 -1149.4759
+ 650 253.31349 -7578.2665 813.75975 -5252.0827 -2915.5706
+ 700 256.61152 -7588.1475 761.03356 -5294.9988 -747.88089
+ 750 248.3606 -7660.457 837.71615 -5339.8883 -3072.8311
+ 800 253.81464 -7638.6089 782.4229 -5340.7698 -1025.909
+ 850 245.69185 -7660.9036 795.66792 -5398.3172 -2717.5851
+ 900 249.13156 -7589.4769 806.43464 -5295.5867 -761.63361
+ 950 251.11482 -7691.4981 869.34937 -5322.852 -3282.3031
+ 1000 241.9195 -7630.9899 828.59107 -5358.0033 -95.962685
+Loop time of 45.5507 on 4 procs for 1000 steps with 2004 atoms
+
+Performance: 15.174 ns/day, 1.582 hours/ns, 21.954 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 35.545 | 36.674 | 38.004 | 15.8 | 80.51
+Bond | 0.51302 | 0.67796 | 0.86345 | 18.6 | 1.49
+Kspace | 0.66031 | 0.68459 | 0.70506 | 2.1 | 1.50
+Neigh | 1.5605 | 1.5627 | 1.5649 | 0.1 | 3.43
+Comm | 3.4611 | 4.9841 | 6.294 | 47.2 | 10.94
+Output | 0.00079799 | 0.00086641 | 0.0010369 | 0.0 | 0.00
+Modify | 0.67341 | 0.69059 | 0.71186 | 1.7 | 1.52
+Other | | 0.2762 | | | 0.61
+
+Nlocal: 501 ave 523 max 473 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Nghost: 6643.25 ave 6708 max 6566 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs: 176977 ave 185765 max 164931 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 707908
+Ave neighs/atom = 353.248
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 200
+unfix cor
+unfix 1
+
+
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:45
diff --git a/src/.gitignore b/src/.gitignore
index 1c7f468e6e4888178b0c4abf8f1311506dff77d2..557c01c95f88c72b51e65dfe242e836b2257111c 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -328,6 +328,8 @@
/fix_eos_table.h
/fix_evaporate.cpp
/fix_evaporate.h
+/fix_filter_corotate.cpp
+/fix_filter_corotate.h
/fix_viscosity.cpp
/fix_viscosity.h
/fix_ehex.cpp
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 52ee6cad9467af17133a9d4ad86e61dddc3931bc..72d93aee2b3b83e14c1302f7b6eb6b46c99de699 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -38,6 +38,7 @@ dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16
dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
+fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017
fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016
fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
fix grem, David Stelter, dstelter@bu.edu, 22 Nov 16
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b59a37e8f9fcf04211e7cc1830b0e864c8f746ae
--- /dev/null
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -0,0 +1,2017 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Lukas Fath (KIT)
+ some subroutines are from fix_shake.cpp
+ ------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
+#include "fix_filter_corotate.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "bond.h"
+#include "angle.h"
+#include "math_const.h"
+#include "update.h"
+#include "modify.h"
+#include "domain.h"
+#include "region.h"
+#include "memory.h"
+#include "error.h"
+#include "force.h"
+#include "comm.h"
+#include "error.h"
+#include "memory.h"
+#include "domain.h"
+#include "integrate.h"
+#include "respa.h"
+#include "neighbor.h"
+#include "citeme.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+using namespace FixConst;
+
+// allocate space for static class variable
+
+FixFilterCorotate *FixFilterCorotate::fsptr = NULL;
+
+#define BIG 1.0e20
+#define MASSDELTA 0.1
+
+static const char cite_filter_corotate[] =
+ "Mollified Impulse Method with Corotational Filter:\n\n"
+ "@Article{Fath2017,\n"
+ " Title ="
+ "{A fast mollified impulse method for biomolecular atomistic simulations},\n"
+ " Author = {L. Fath and M. Hochbruck and C.V. Singh},\n"
+ " Journal = {Journal of Computational Physics},\n"
+ " Year = {2017},\n"
+ " Pages = {180 - 198},\n"
+ " Volume = {333},\n\n"
+ " Doi = {http://dx.doi.org/10.1016/j.jcp.2016.12.024},\n"
+ " ISSN = {0021-9991},\n"
+ " Keywords = {Mollified impulse method},\n"
+ " Url = {http://www.sciencedirect.com/science/article/pii/S0021999116306787}\n"
+ "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+FixFilterCorotate::FixFilterCorotate(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp,narg,arg)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_filter_corotate);
+
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ molecular = atom->molecular;
+ if (molecular == 0)
+ error->all(FLERR,"Cannot use fix filter/corotate "
+ "with non-molecular system");
+ if (molecular == 2)
+ error->all(FLERR,"Cannot use fix filter/corotate "
+ "with molecular template system");
+
+ // parse args for bond and angle types
+ // will be used by find_clusters
+ // store args for "b" "a" "t" as flags in (1:n) list for fast access
+ // store args for "m" in list of length nmass for looping over
+ // for "m" verify that atom masses have been set
+
+ bond_flag = new int[atom->nbondtypes+1];
+ for (int i = 1; i <= atom->nbondtypes; i++) bond_flag[i] = 0;
+ angle_flag = new int[atom->nangletypes+1];
+ for (int i = 1; i <= atom->nangletypes; i++) angle_flag[i] = 0;
+ type_flag = new int[atom->ntypes+1];
+ for (int i = 1; i <= atom->ntypes; i++) type_flag[i] = 0;
+ mass_list = new double[atom->ntypes];
+ nmass = 0;
+
+ char mode = '\0';
+ int next = 3;
+ while (next < narg) {
+ if (strcmp(arg[next],"b") == 0) mode = 'b';
+ else if (strcmp(arg[next],"a") == 0) mode = 'a';
+ else if (strcmp(arg[next],"t") == 0) mode = 't';
+ else if (strcmp(arg[next],"m") == 0) {
+ mode = 'm';
+ atom->check_mass(FLERR);
+
+ // break if keyword that is not b,a,t,m
+
+ } else if (isalpha(arg[next][0])) break;
+
+ // read numeric args of b,a,t,m
+
+ else if (mode == 'b') {
+ int i = force->inumeric(FLERR,arg[next]);
+ if (i < 1 || i > atom->nbondtypes)
+ error->all(FLERR,"Invalid bond type index for fix filter/corotate");
+ bond_flag[i] = 1;
+
+ } else if (mode == 'a') {
+ int i = force->inumeric(FLERR,arg[next]);
+ if (i < 1 || i > atom->nangletypes)
+ error->all(FLERR,"Invalid angle type index for fix filter/corotate");
+ angle_flag[i] = 1;
+
+ } else if (mode == 't') {
+ int i = force->inumeric(FLERR,arg[next]);
+ if (i < 1 || i > atom->ntypes)
+ error->all(FLERR,"Invalid atom type index for fix filter/corotate");
+ type_flag[i] = 1;
+
+ } else if (mode == 'm') {
+ double massone = force->numeric(FLERR,arg[next]);
+ if (massone == 0.0)
+ error->all(FLERR,"Invalid atom mass for fix filter/corotate");
+ if (nmass == atom->ntypes)
+ error->all(FLERR,"Too many masses for fix filter/corotate");
+ mass_list[nmass++] = massone;
+
+ } else error->all(FLERR,"Illegal fix filter/corotate command");
+ next++;
+ }
+
+
+ // parse optional args
+ nlevels_respa = 1; //initialize
+
+ // allocate bond and angle distance arrays, indexed from 1 to n
+
+ bond_distance = new double[atom->nbondtypes+1];
+ angle_distance = new double[atom->nangletypes+1];
+
+ //grow_arrays
+ array_atom = NULL;
+ shake_flag = NULL;
+ shake_atom = NULL;
+ shake_type = NULL;
+
+ grow_arrays(atom->nmax);
+ atom->add_callback(0); //calls grow_arrays
+
+ x_store = NULL;
+
+ //STUFF
+ g = NULL;
+ help2 = NULL;
+
+ dn1dx = dn2dx = dn3dx = NULL;
+ n1 = n2 = n3 = del1 = del2 = del3 = NULL;
+
+ memory->grow(help2,15,15,"FilterCorotate:help2");
+ memory->grow(n1,3,"FilterCorotate:n1");
+ memory->grow(n2,3,"FilterCorotate:n2");
+ memory->grow(n3,3,"FilterCorotate:n3");
+ memory->grow(del1,3,"FilterCorotate:del1");
+ memory->grow(del2,3,"FilterCorotate:del2");
+ memory->grow(del3,3,"FilterCorotate:del3");
+ memory->grow(dn1dx,3,15,"FilterCorotate:dn1dx");
+ memory->grow(dn2dx,3,15,"FilterCorotate:dn2dx");
+ memory->grow(dn3dx,3,15,"FilterCorotate:dn3dx");
+
+ memory->grow(g,15,"FilterCorotate:g");
+
+ comm_forward = 3;
+
+ // identify all clusters
+
+ find_clusters();
+
+ // initialize list of clusters to constrain
+
+ maxlist = 0;
+ list = NULL;
+ clist_derv = NULL;
+ clist_q0 = NULL; //list for derivative and ref. config
+ clist_nselect1 = clist_nselect2 = NULL;
+ clist_select1 = clist_select2 = NULL;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixFilterCorotate::~FixFilterCorotate()
+{
+ memory->destroy(g);
+ memory->destroy(help2);
+ memory->destroy(n1);
+ memory->destroy(n2);
+ memory->destroy(n3);
+ memory->destroy(del1);
+ memory->destroy(del2);
+ memory->destroy(del3);
+ memory->destroy(dn1dx);
+ memory->destroy(dn2dx);
+ memory->destroy(dn3dx);
+
+ atom->delete_callback(id,2);
+ atom->delete_callback(id,0);
+
+ // delete locally stored arrays
+
+ memory->destroy(shake_flag);
+ memory->destroy(shake_atom);
+ memory->destroy(shake_type);
+ memory->destroy(array_atom);
+
+ delete [] bond_flag;
+ delete [] angle_flag;
+ delete [] type_flag;
+ delete [] mass_list;
+
+ delete [] bond_distance;
+ delete [] angle_distance;
+
+ memory->destroy(list);
+ memory->destroy(clist_derv);
+ memory->destroy(clist_q0);
+ memory->destroy(clist_nselect1);
+ memory->destroy(clist_nselect2);
+ memory->destroy(clist_select1);
+ memory->destroy(clist_select2);
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+int FixFilterCorotate::setmask()
+{
+ int mask = 0;
+
+ mask |= PRE_NEIGHBOR;
+ mask |= PRE_FORCE_RESPA;
+ mask |= POST_FORCE_RESPA;
+
+ return mask;
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixFilterCorotate::init()
+{
+ int i;
+ // error if more than one filter
+ int count = 0;
+ for (i = 0; i < modify->nfix; i++){
+ if (strcmp(modify->fix[i]->style,"filter/corotate") == 0) count++;
+ }
+ if (count > 1) error->all(FLERR,"More than one fix filter/corotate");
+
+ // check for fix shake:
+ count = 0;
+ for (i = 0; i < modify->nfix; i++){
+ if (strcmp(modify->fix[i]->style,"shake") == 0) count++;
+ }
+ if (count > 1)
+ error->one(FLERR,"Both fix shake and fix filter/corotate detected.");
+
+ // if rRESPA, find associated fix that must exist
+ // could have changed locations in fix list since created
+ // set ptrs to rRESPA variables
+
+ if (strstr(update->integrate_style,"respa")) {
+ nlevels_respa = ((Respa *) update->integrate)->nlevels;
+ }
+ else error->all(FLERR,"Fix filter/corotate requires rRESPA!");
+
+ // set equilibrium bond distances
+
+ if (force->bond == NULL)
+ error->all(FLERR,"Bond potential must be defined for fix filter/corotate");
+ for (i = 1; i <= atom->nbondtypes; i++)
+ bond_distance[i] = force->bond->equilibrium_distance(i);
+
+ // set equilibrium angle value
+
+ for (i = 1; i <= atom->nangletypes; i++) {
+ angle_distance[i] = force->angle->equilibrium_angle(i);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * pre-integrator setup
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::setup_pre_neighbor()
+{
+ pre_neighbor();
+}
+
+
+/* ----------------------------------------------------------------------
+ * build list of clusters to constrain
+ * if one or more atoms in cluster are on this proc,
+ * this proc lists the cluster exactly once
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::pre_neighbor()
+{
+ int atom1,atom2,atom3,atom4,atom5;
+
+ // local copies of atom quantities
+ // used until next re-neighboring
+
+ x = atom->x;
+ v = atom->v;
+ f = atom->f;
+ mass = atom->mass;
+ rmass = atom->rmass;
+ type = atom->type;
+ nlocal = atom->nlocal;
+
+ // extend size of list if necessary
+
+ if (nlocal > maxlist) {
+ maxlist = nlocal;
+
+ memory->destroy(list);
+ memory->destroy(clist_derv);
+ memory->destroy(clist_q0);
+ memory->destroy(clist_nselect1);
+ memory->destroy(clist_nselect2);
+ memory->destroy(clist_select1);
+ memory->destroy(clist_select2);
+
+ memory->create(list,maxlist,"FilterCorotate:list");
+ memory->create(clist_derv,maxlist,15,15,"FilterCorotate:derivative");
+ memory->create(clist_q0,maxlist,15,"FilterCorotate:q0");
+ memory->create(clist_nselect1,maxlist,"FilterCorotate:nselect1");
+ memory->create(clist_nselect2,maxlist,"FilterCorotate:nselect2");
+ memory->create(clist_select1,maxlist,5,"FilterCorotate:select1");
+ memory->create(clist_select2,maxlist,5,"FilterCorotate:select2");
+ }
+
+ // build list of clusters I compute
+
+ nlist = 0;
+
+ for (int i = 0; i < nlocal; i++){
+ if (shake_flag[i]) {
+ if (shake_flag[i] == 2) {
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ if (atom1 == -1 || atom2 == -1) {
+ char str[128];
+ sprintf(str,"Cluster atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2) list[nlist++] = i;
+ } else if (shake_flag[i] == 1 || shake_flag[i] == 3) {
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ atom3 = atom->map(shake_atom[i][2]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
+ char str[128];
+ sprintf(str,"Cluster atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
+ } else if (shake_flag[i] == 4) {
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ atom3 = atom->map(shake_atom[i][2]);
+ atom4 = atom->map(shake_atom[i][3]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+ char str[128];
+ sprintf(str,"Cluster atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],
+ shake_atom[i][2],shake_atom[i][3],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
+ list[nlist++] = i;
+ } else if (shake_flag[i] == 5) {
+ atom1 = atom->map(shake_atom[i][0]);
+ atom2 = atom->map(shake_atom[i][1]);
+ atom3 = atom->map(shake_atom[i][2]);
+ atom4 = atom->map(shake_atom[i][3]);
+ atom5 = atom->map(shake_atom[i][4]);
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 ||
+ atom4 == -1 || atom5 == -1) {
+ char str[128];
+ sprintf(str,"Cluster atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ shake_atom[i][0],shake_atom[i][1],
+ shake_atom[i][2],shake_atom[i][3],shake_atom[i][4],
+ me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4 && i <= atom5)
+ list[nlist++] = i;
+ }
+ }
+ }
+
+ //also build reference config lists
+ int m,N,oxy;
+ double r0,r1,r2,theta0;
+ double m1,m2,m3,m4,m5,m_all;
+
+ double *mass = atom->mass;
+ int *type = atom->type;
+
+ for (int i=0; i<nlist; i++)
+ {
+ m = list[i];
+ N = shake_flag[m];
+
+ //switch cluster type 3 to angle cluster:
+ if (N == 3)
+ {
+ //make it an angle cluster:
+ if (shake_type[m][2] == 0)
+ shake_type[m][2] = angletype_findset(atom->map(shake_atom[m][0]),
+ shake_atom[m][1],shake_atom[m][2],0);
+ }
+
+ if (N == 1) N = 3; //angle cluster
+
+ if (N == 2) //cluster of size 2:
+ {
+ atom1 = atom->map(shake_atom[m][0]);
+ atom2 = atom->map(shake_atom[m][1]);
+
+ r0 = bond_distance[shake_type[m][0]];
+
+ m1 = mass[type[atom1]];
+ m2 = mass[type[atom2]];
+ m_all = m1 + m2;
+
+ double a1 = -m2/(m1+m2)*r0;
+ double a2 = m1/(m1+m2)*r0;
+
+ clist_q0[i][0] = a1;
+ clist_q0[i][1] = 0;
+ clist_q0[i][2] = 0;
+
+ clist_q0[i][3] = a2;
+ clist_q0[i][4] = 0;
+ clist_q0[i][5] = 0;
+
+ clist_nselect1[i] = 1;
+ clist_select1[i][0] = 1;
+
+ clist_nselect2[i] = 0;
+ clist_select2[i][0] = 0;
+ } else if (N == 3) //angle cluster
+ {
+ oxy = atom->map(shake_atom[m][0]);
+ atom1 = atom->map(shake_atom[m][1]);
+ atom2 = atom->map(shake_atom[m][2]);
+
+ r0 = bond_distance[shake_type[m][0]];
+ r1 = bond_distance[shake_type[m][1]];
+
+
+ theta0 = angle_distance[shake_type[m][2]];
+
+ m1 = mass[type[oxy]];
+ m2 = mass[type[atom1]];
+ m3 = mass[type[atom2]];
+ m_all = m1 + m2 + m3;
+
+ double alpha1 = 0.5*(MY_PI - theta0);
+
+ double xcenter = m2/m_all*r0*sin(alpha1) + m3/m_all*r1*sin(alpha1);
+ double ycenter = -m2/m_all*r0*cos(alpha1)+ m3/m_all*r1*cos(alpha1);
+
+ double q1 = -xcenter;
+ double q2 = -ycenter;
+
+ double q4 = r0*sin(alpha1)-xcenter;
+ double q5 = r0*cos(alpha1)-ycenter;
+
+ double q7 = r1*sin(alpha1)-xcenter;
+ double q8 = -r1*cos(alpha1)-ycenter;
+
+ clist_q0[i][0] = q1;
+ clist_q0[i][1] = q2;
+ clist_q0[i][2] = 0;
+
+ clist_q0[i][3] = q4;
+ clist_q0[i][4] = q5;
+ clist_q0[i][5] = 0;
+
+ clist_q0[i][6] = q7;
+ clist_q0[i][7] = q8;
+ clist_q0[i][8] = 0;
+
+ clist_nselect1[i] = 2;
+ clist_select1[i][0] = 1; clist_select1[i][1] = 2;
+ clist_nselect2[i] = 1;
+ clist_select2[i][0] = 1;
+ } else if (N == 4)
+ {
+ oxy = atom->map(shake_atom[m][0]);
+ atom1 = atom->map(shake_atom[m][1]);
+ atom2 = atom->map(shake_atom[m][2]);
+ atom3 = atom->map(shake_atom[m][3]);
+
+ r0 = bond_distance[shake_type[m][0]];
+ r1 = bond_distance[shake_type[m][1]];
+ r2 = bond_distance[shake_type[m][2]];
+
+ m1 = atom->mass[atom->type[oxy]];
+ m2 = atom->mass[atom->type[atom1]];
+ m3 = atom->mass[atom->type[atom2]];
+ m4 = atom->mass[atom->type[atom3]];
+ m_all = m1 + m2 + m3 + m4;
+
+ //how to get these angles?
+ double alpha1 = MY_PI/2.57; //roughly 70 degrees
+ double alpha2 = MY_PI/3;
+ //ENSURE ycenter,zcenter = 0!
+ //approximate xcenter, if r0 !=r1 != r2, exact if r0 = r1 = r2
+ double xcenter = (m2*r0+m3*r1+m4*r2)/m_all*cos(alpha1);
+
+ clist_q0[i][0] = -xcenter;
+ clist_q0[i][1] = 0.0;
+ clist_q0[i][2] = 0.0;
+ clist_q0[i][3] = r0*cos(alpha1)-xcenter;
+ clist_q0[i][4] = -r0*sin(alpha1);
+ clist_q0[i][5] = 0.0;
+ clist_q0[i][6] = r1*cos(alpha1)-xcenter;
+ clist_q0[i][7] = r1*sin(alpha1)*cos(alpha2);
+ clist_q0[i][8] = -r1*sin(alpha1)*sin(alpha2);
+ clist_q0[i][9] = r2*cos(alpha1)-xcenter;
+ clist_q0[i][10] = r2*sin(alpha1)*cos(alpha2);
+ clist_q0[i][11] = r2*sin(alpha1)*sin(alpha2);
+
+ clist_nselect1[i] = 3;
+ clist_nselect2[i] = 2;
+
+ clist_select1[i][0] = 1;clist_select1[i][1] = 2;clist_select1[i][2] = 3;
+ clist_select2[i][0] = 2;clist_select2[i][1] = 3;
+
+ //signum ensures correct ordering of three satellites
+ //signum = sign(cross(x2-x1,x3-x1))T*(x1-x0))
+ double del1[3], del2[3], del3[3];
+ del1[0] = x[atom1][0]-x[oxy][0];
+ del1[1] = x[atom1][1]-x[oxy][1];
+ del1[2] = x[atom1][2]-x[oxy][2];
+ domain->minimum_image(del1);
+
+ del2[0] = x[atom2][0]-x[atom1][0];
+ del2[1] = x[atom2][1]-x[atom1][1];
+ del2[2] = x[atom2][2]-x[atom1][2];
+ domain->minimum_image(del2);
+
+ del3[0] = x[atom3][0]-x[atom1][0];
+ del3[1] = x[atom3][1]-x[atom1][1];
+ del3[2] = x[atom3][2]-x[atom1][2];
+ domain->minimum_image(del3);
+
+ double a = (del2[1])*(del3[2]) - (del2[2])*(del3[1]);
+ double b = (del2[2])*(del3[0]) - (del2[0])*(del3[2]);
+ double c = (del2[0])*(del3[1]) - (del2[1])*(del3[0]);
+ int signum = sgn(a*(del1[0]) + b*(del1[1]) + c*(del1[2]));
+
+ if (fabs(signum)!= 1)
+ error->all(FLERR,"Wrong orientation in cluster of size 4"
+ "in fix filter/corotate!");
+ clist_q0[i][8] *= signum;
+ clist_q0[i][11] *= signum;
+
+ } else if (N == 5)
+ {
+ oxy = atom->map(shake_atom[m][0]);
+ atom1 = atom->map(shake_atom[m][1]);
+ atom2 = atom->map(shake_atom[m][2]);
+ atom3 = atom->map(shake_atom[m][3]);
+ int c1 = atom->map(shake_atom[m][4]);
+
+ r1 = bond_distance[shake_type[m][3]];
+ r0 = bond_distance[shake_type[m][0]];
+ theta0 = angle_distance[shake_type[m][2]];
+
+ m1 = atom->mass[atom->type[oxy]];
+ m2 = atom->mass[atom->type[atom1]];
+ m3 = atom->mass[atom->type[atom2]];
+ m4 = atom->mass[atom->type[atom3]];
+ m5 = atom->mass[atom->type[c1]];
+ m_all = m1 + m2 + m3 + m4 + m5;
+
+ double alpha1 = MY_PI/2.57; //roughly 70 degrees
+ double alpha2 = MY_PI/3;
+ //ENSURE ycenter,zcenter = 0!
+ double xcenter = -(m2+m3+m4)/m_all*r0*cos(alpha1) +r1*m5/m_all;
+
+ clist_q0[i][0] = -xcenter;
+ clist_q0[i][1] = 0.0;
+ clist_q0[i][2] = 0.0;
+ clist_q0[i][3] = -r0*cos(alpha1)-xcenter;
+ clist_q0[i][4] = -r0*sin(alpha1);
+ clist_q0[i][5] = 0.0;
+ clist_q0[i][6] = -r0*cos(alpha1)-xcenter;
+ clist_q0[i][7] = r0*sin(alpha1)*cos(alpha2);
+ clist_q0[i][8] = r0*sin(alpha1)*sin(alpha2);
+ clist_q0[i][9] = -r0*cos(alpha1)-xcenter;
+ clist_q0[i][10] = r0*sin(alpha1)*cos(alpha2);
+ clist_q0[i][11] = -r0*sin(alpha1)*sin(alpha2);
+ clist_q0[i][12] = r1-xcenter;
+ clist_q0[i][13] = 0.0;
+ clist_q0[i][14] = 0.0;
+ clist_nselect1[i] = 1;
+ clist_nselect2[i] = 2;
+
+ clist_select1[i][0] = 4;
+ clist_select2[i][0] = 2;clist_select2[i][1] = 3;
+
+ //signum ensures correct ordering of three satellites
+ //signum = sign(cross(x2-x1,x3-x1))T*(x1-x0))
+ double del1[3], del2[3], del3[3];
+ del1[0] = x[atom1][0]-x[oxy][0];
+ del1[1] = x[atom1][1]-x[oxy][1];
+ del1[2] = x[atom1][2]-x[oxy][2];
+ domain->minimum_image(del1);
+
+ del2[0] = x[atom2][0]-x[atom1][0];
+ del2[1] = x[atom2][1]-x[atom1][1];
+ del2[2] = x[atom2][2]-x[atom1][2];
+ domain->minimum_image(del2);
+
+ del3[0] = x[atom3][0]-x[atom1][0];
+ del3[1] = x[atom3][1]-x[atom1][1];
+ del3[2] = x[atom3][2]-x[atom1][2];
+ domain->minimum_image(del3);
+
+ double a = (del2[1])*(del3[2]) - (del2[2])*(del3[1]);
+ double b = (del2[2])*(del3[0]) - (del2[0])*(del3[2]);
+ double c = (del2[0])*(del3[1]) - (del2[1])*(del3[0]);
+ int signum = sgn(a*(del1[0]) + b*(del1[1]) + c*(del1[2]));
+
+ if (fabs(signum)!= 1)
+ error->all(FLERR,"Wrong orientation in cluster of size 5"
+ "in fix filter/corotate!");
+ clist_q0[i][8] *= signum;
+ clist_q0[i][11] *= signum;
+ }
+ else
+ {
+ error->all(FLERR,"Fix filter/corotate cluster with size > 5"
+ "not yet configured...");
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * setup, needs to patch missing setup_post_force_respa() in respa...
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::setup(int vflag)
+{
+ ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
+ post_force_respa(vflag,nlevels_respa-1,0);
+ ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
+}
+
+void FixFilterCorotate::setup_pre_force_respa(int vflag,int ilevel){
+ pre_force_respa(vflag,ilevel,0);
+}
+
+//void FixFilterCorotate::setup_post_force_respa(int vflag,int ilevel){
+// post_force_respa(vflag,ilevel,0);
+//}
+
+double FixFilterCorotate::compute_array(int,int)
+{
+ filter_inner();
+ return 1;
+}
+
+void FixFilterCorotate::pre_force_respa(int vflag, int ilevel, int iloop)
+{
+ if (ilevel == nlevels_respa-1)
+ {
+ filter_inner();
+
+ //%Switch pointers x<-->x_filter
+ x_store = atom->x;
+ atom->x = array_atom;
+ }
+}
+
+void FixFilterCorotate::post_force_respa(int vflag, int ilevel, int iloop)
+{
+ if (ilevel == nlevels_respa-1)
+ {
+ atom->x = x_store;
+
+ comm->forward_comm_fix(this); //comm forward of forces for outer filter
+
+ filter_outer();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixFilterCorotate::filter_inner()
+{
+ int nall = atom->nlocal + atom->nghost;
+ double **x = atom->x;
+
+ //set array_atom to atom->x, in case some atoms are not part of any cluster:
+ for (int i=0; i<nall; i++)
+ {
+ array_atom[i][0] = x[i][0];
+ array_atom[i][1] = x[i][1];
+ array_atom[i][2] = x[i][2];
+ }
+
+ int m;
+ //iterate through list:
+ for (int i=0; i<nlist; i++)
+ {
+ m = list[i];
+
+ //filter:
+ general_cluster(m,i);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixFilterCorotate::filter_outer()
+{
+ double sum1,sum2,sum3;
+ double** f = atom->f;
+ int m;
+
+ for (int i=0; i<nlist; i++)
+ {
+ m = list[i];
+ int dim = shake_flag[m];
+ if (dim == 1) //case: angle
+ dim = 3;
+
+ for (int j = 0; j < dim; j++)
+ {
+ sum1 = sum2 = sum3 = 0;
+ for (int k = 0; k < dim; k++)
+ {
+ //get local tag of k-th atom in cluster i:
+ int kk = atom->map(shake_atom[m][k]);
+ //apply derivative times force
+ sum1 += clist_derv[i][3*j][3*k]*f[kk][0]+clist_derv[i][3*j][3*k+1]*
+ f[kk][1]+clist_derv[i][3*j][3*k+2]*f[kk][2];
+ sum2 += clist_derv[i][3*j+1][3*k]*f[kk][0]+clist_derv[i][3*j+1][3*k+1]*
+ f[kk][1]+clist_derv[i][3*j+1][3*k+2]*f[kk][2];
+ sum3 += clist_derv[i][3*j+2][3*k]*f[kk][0]+clist_derv[i][3*j+2][3*k+1]*
+ f[kk][1]+clist_derv[i][3*j+2][3*k+2]*f[kk][2];
+ }
+
+ g[3*j] = sum1;
+ g[3*j+1] = sum2;
+ g[3*j+2] = sum3;
+ }
+
+ //replace force f with filtered value:
+ for (int j = 0; j < dim; j++)
+ {
+ int kk = atom->map(shake_atom[m][j]);
+
+ f[kk][0] = g[3*j];
+ f[kk][1] = g[3*j+1];
+ f[kk][2] = g[3*j+2];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * identify whether each atom is in a SHAKE cluster
+ * only include atoms in fix group and those bonds/angles specified in input
+ * test whether all clusters are valid
+ * set shake_flag, shake_atom, shake_type values
+ * set bond,angle types negative so will be ignored in neighbor lists
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::find_clusters()
+{
+ int i,j,m,n;
+ int flag,flag_all,nbuf,size;
+ double massone;
+ tagint *buf;
+
+ if (me == 0 && screen)
+ fprintf(screen,"Finding filter clusters ...\n");
+
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ double *mass = atom->mass;
+ double *rmass = atom->rmass;
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+
+ int nlocal = atom->nlocal;
+ int angles_allow = atom->avec->angles_allow;
+
+ // setup ring of procs
+
+ int next = me + 1;
+ int prev = me -1;
+ if (next == nprocs) next = 0;
+ if (prev < 0) prev = nprocs - 1;
+
+ // -----------------------------------------------------
+ // allocate arrays for self (1d) and bond partners (2d)
+ // max = max # of bond partners for owned atoms = 2nd dim of partner arrays
+ // npartner[i] = # of bonds attached to atom i
+ // nshake[i] = # of SHAKE bonds attached to atom i
+ // partner_tag[i][] = global IDs of each partner
+ // partner_mask[i][] = mask of each partner
+ // partner_type[i][] = type of each partner
+ // partner_massflag[i][] = 1 if partner meets mass criterion, 0 if not
+ // partner_bondtype[i][] = type of bond attached to each partner
+ // partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
+ // partner_nshake[i][] = nshake value for each partner
+ // -----------------------------------------------------
+
+ int max = 0;
+
+ for (i = 0; i < nlocal; i++) max = MAX(max,nspecial[i][0]);
+
+ int *npartner;
+ memory->create(npartner,nlocal,"shake:npartner");
+ memory->create(nshake,nlocal,"shake:nshake");
+
+ tagint **partner_tag;
+ int **partner_mask,**partner_type,**partner_massflag;
+ int **partner_bondtype,**partner_shake,**partner_nshake;
+ memory->create(partner_tag,nlocal,max,"shake:partner_tag");
+ memory->create(partner_mask,nlocal,max,"shake:partner_mask");
+ memory->create(partner_type,nlocal,max,"shake:partner_type");
+ memory->create(partner_massflag,nlocal,max,"shake:partner_massflag");
+ memory->create(partner_bondtype,nlocal,max,"shake:partner_bondtype");
+ memory->create(partner_shake,nlocal,max,"shake:partner_shake");
+ memory->create(partner_nshake,nlocal,max,"shake:partner_nshake");
+
+ // -----------------------------------------------------
+ // set npartner and partner_tag from special arrays
+ // -----------------------------------------------------
+
+ for (i = 0; i < nlocal; i++) {
+ npartner[i] = nspecial[i][0];
+ for (j = 0; j < npartner[i]; j++)
+ partner_tag[i][j] = special[i][j];
+ }
+
+ // -----------------------------------------------------
+ // set partner_mask, partner_type, partner_massflag, partner_bondtype
+ // for bonded partners
+ // requires communication for off-proc partners
+ // -----------------------------------------------------
+
+ // fill in mask, type, massflag, bondtype if own bond partner
+ // info to store in buf for each off-proc bond = nper = 6
+ // 2 atoms IDs in bond, space for mask, type, massflag, bondtype
+ // nbufmax = largest buffer needed to hold info from any proc
+
+ int nper = 6;
+
+ nbuf = 0;
+ for (i = 0; i < nlocal; i++) {
+ for (j = 0; j < npartner[i]; j++) {
+ partner_mask[i][j] = 0;
+ partner_type[i][j] = 0;
+ partner_massflag[i][j] = 0;
+ partner_bondtype[i][j] = 0;
+
+ m = atom->map(partner_tag[i][j]);
+ if (m >= 0 && m < nlocal) {
+ partner_mask[i][j] = mask[m];
+ partner_type[i][j] = type[m];
+ if (nmass) {
+ if (rmass) massone = rmass[m];
+ else massone = mass[type[m]];
+ partner_massflag[i][j] = masscheck(massone);
+ }
+ n = bondtype_findset(i,tag[i],partner_tag[i][j],0);
+ if (n) partner_bondtype[i][j] = n;
+ else {
+ n = bondtype_findset(m,tag[i],partner_tag[i][j],0);
+ if (n) partner_bondtype[i][j] = n;
+ }
+ } else nbuf += nper;
+ }
+ }
+
+ memory->create(buf,nbuf,"filter/corotate:buf");
+
+ // fill buffer with info
+
+ size = 0;
+ for (i = 0; i < nlocal; i++) {
+ for (j = 0; j < npartner[i]; j++) {
+ m = atom->map(partner_tag[i][j]);
+ if (m < 0 || m >= nlocal) {
+ buf[size] = tag[i];
+ buf[size+1] = partner_tag[i][j];
+ buf[size+2] = 0;
+ buf[size+3] = 0;
+ buf[size+4] = 0;
+ n = bondtype_findset(i,tag[i],partner_tag[i][j],0);
+ if (n) buf[size+5] = n;
+ else buf[size+5] = 0;
+ size += nper;
+ }
+ }
+ }
+
+ // cycle buffer around ring of procs back to self
+
+ fsptr = this;
+ comm->ring(size,sizeof(tagint),buf,1,ring_bonds,buf);
+
+ // store partner info returned to me
+
+ m = 0;
+ while (m < size) {
+ i = atom->map(buf[m]);
+ for (j = 0; j < npartner[i]; j++){
+ if (buf[m+1] == partner_tag[i][j]) break;
+ }
+ partner_mask[i][j] = buf[m+2];
+ partner_type[i][j] = buf[m+3];
+ partner_massflag[i][j] = buf[m+4];
+ partner_bondtype[i][j] = buf[m+5];
+ m += nper;
+ }
+
+ memory->destroy(buf);
+
+ // error check for unfilled partner info
+ // if partner_type not set, is an error
+ // partner_bondtype may not be set if special list is not consistent
+ // with bondatom (e.g. due to delete_bonds command)
+ // this is OK if one or both atoms are not in fix group, since
+ // bond won't be SHAKEn anyway
+ // else it's an error
+
+ flag = 0;
+ for (i = 0; i < nlocal; i++){
+ for (j = 0; j < npartner[i]; j++) {
+ if (partner_type[i][j] == 0) flag = 1;
+ if (!(mask[i] & groupbit)) continue;
+ if (!(partner_mask[i][j] & groupbit)) continue;
+ if (partner_bondtype[i][j] == 0) flag = 1;
+ }
+ }
+
+ MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+ if (flag_all)
+ error->all(FLERR,"Did not find fix filter/corotate partner info");
+
+ // -----------------------------------------------------
+ // identify SHAKEable bonds
+ // set nshake[i] = # of SHAKE bonds attached to atom i
+ // set partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
+ // both atoms must be in group, bondtype must be > 0
+ // check if bondtype is in input bond_flag
+ // check if type of either atom is in input type_flag
+ // check if mass of either atom is in input mass_list
+ // -----------------------------------------------------
+
+ int np;
+
+ for (i = 0; i < nlocal; i++) {
+ nshake[i] = 0;
+ np = npartner[i];
+ for (j = 0; j < np; j++) {
+ partner_shake[i][j] = 0;
+
+ if (!(mask[i] & groupbit)) continue;
+ if (!(partner_mask[i][j] & groupbit)) continue;
+ if (partner_bondtype[i][j] <= 0) continue;
+
+ if (bond_flag[partner_bondtype[i][j]]) {
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
+ }
+ if (type_flag[type[i]] || type_flag[partner_type[i][j]]) {
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
+ }
+ if (nmass) {
+ if (partner_massflag[i][j]) {
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
+ } else {
+ if (rmass) massone = rmass[i];
+ else massone = mass[type[i]];
+ if (masscheck(massone)) {
+ partner_shake[i][j] = 1;
+ nshake[i]++;
+ continue;
+ }
+ }
+ }
+ }
+ }
+
+ // -----------------------------------------------------
+ // set partner_nshake for bonded partners
+ // requires communication for off-proc partners
+ // -----------------------------------------------------
+
+ // fill in partner_nshake if own bond partner
+ // info to store in buf for each off-proc bond =
+ // 2 atoms IDs in bond, space for nshake value
+ // nbufmax = largest buffer needed to hold info from any proc
+
+ nbuf = 0;
+ for (i = 0; i < nlocal; i++) {
+ for (j = 0; j < npartner[i]; j++) {
+ m = atom->map(partner_tag[i][j]);
+ if (m >= 0 && m < nlocal) partner_nshake[i][j] = nshake[m];
+ else nbuf += 3;
+ }
+ }
+
+ memory->create(buf,nbuf,"filter/corotate:buf");
+
+ // fill buffer with info
+
+ size = 0;
+ for (i = 0; i < nlocal; i++) {
+ for (j = 0; j < npartner[i]; j++) {
+ m = atom->map(partner_tag[i][j]);
+ if (m < 0 || m >= nlocal) {
+ buf[size] = tag[i];
+ buf[size+1] = partner_tag[i][j];
+ size += 3;
+ }
+ }
+ }
+
+ // cycle buffer around ring of procs back to self
+
+ fsptr = this;
+ comm->ring(size,sizeof(tagint),buf,2,ring_nshake,buf);
+
+ // store partner info returned to me
+
+ m = 0;
+ while (m < size) {
+ i = atom->map(buf[m]);
+ for (j = 0; j < npartner[i]; j++){
+ if (buf[m+1] == partner_tag[i][j]) break;
+ }
+ partner_nshake[i][j] = buf[m+2];
+ m += 3;
+ }
+
+ memory->destroy(buf);
+
+ // -----------------------------------------------------
+ // error checks
+ // no atom with nshake > 3
+ // no connected atoms which both have nshake > 1
+ // -----------------------------------------------------
+
+ flag = 0;
+ for (i = 0; i < nlocal; i++) if (nshake[i] > 4) flag = 1;
+ MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+ if (flag_all) error->all(FLERR,"Cluster of more than 5 atoms");
+
+ flag = 0;
+ for (i = 0; i < nlocal; i++) {
+ if (nshake[i] <= 1) continue;
+ for (j = 0; j < npartner[i]; j++)
+ if (partner_shake[i][j] && partner_nshake[i][j] > 1) flag = 1;
+ }
+ MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+ if (flag_all) error->all(FLERR,"Clusters are connected");
+
+ // -----------------------------------------------------
+ // set SHAKE arrays that are stored with atoms & add angle constraints
+ // zero shake arrays for all owned atoms
+ // if I am central atom set shake_flag & shake_atom & shake_type
+ // for 2-atom clusters, I am central atom if my atom ID < partner ID
+ // for 3-atom clusters, test for angle constraint
+ // angle will be stored by this atom if it exists
+ // if angle type matches angle_flag, then it is angle-constrained
+ // shake_flag[] = 0 if atom not in SHAKE cluster
+ // 2,3,4 = size of bond-only cluster
+ // 1 = 3-atom angle cluster
+ // shake_atom[][] = global IDs of 2,3,4 atoms in cluster
+ // central atom is 1st
+ // for 2-atom cluster, lowest ID is 1st
+ // shake_type[][] = bondtype of each bond in cluster
+ // for 3-atom angle cluster, 3rd value is angletype
+ // -----------------------------------------------------
+
+ for (i = 0; i < nlocal; i++) {
+ shake_flag[i] = 0;
+ shake_atom[i][0] = 0;
+ shake_atom[i][1] = 0;
+ shake_atom[i][2] = 0;
+ shake_atom[i][3] = 0;
+ shake_atom[i][4] = 0;
+ shake_type[i][0] = 0;
+ shake_type[i][1] = 0;
+ shake_type[i][2] = 0;
+ shake_type[i][3] = 0;
+
+ if (nshake[i] == 1) {
+ for (j = 0; j < npartner[i]; j++){
+ if (partner_shake[i][j]) break;
+ }
+ if (partner_nshake[i][j] == 1 && tag[i] < partner_tag[i][j]) {
+ shake_flag[i] = 2;
+ shake_atom[i][0] = tag[i];
+ shake_atom[i][1] = partner_tag[i][j];
+ shake_type[i][0] = partner_bondtype[i][j];
+ }
+ }
+
+ if (nshake[i] > 1) {
+ shake_flag[i] = 1;
+ shake_atom[i][0] = tag[i];
+ for (j = 0; j < npartner[i]; j++)
+ if (partner_shake[i][j]) {
+ m = shake_flag[i];
+ shake_atom[i][m] = partner_tag[i][j];
+ shake_type[i][m-1] = partner_bondtype[i][j];
+ shake_flag[i]++;
+ }
+ }
+
+ if (nshake[i] == 2 && angles_allow) {
+ n = angletype_findset(i,shake_atom[i][1],shake_atom[i][2],0);
+ if (n <= 0) continue;
+ //if (angle_flag[n]) { Take all angles!
+ shake_flag[i] = 1;
+ shake_type[i][2] = n;
+ //}
+ }
+ }
+
+ // -----------------------------------------------------
+ // set shake_flag,shake_atom,shake_type for non-central atoms
+ // requires communication for off-proc atoms
+ // -----------------------------------------------------
+
+ // fill in shake arrays for each bond partner I own
+ // info to store in buf for each off-proc bond =
+ // all values from shake_flag, shake_atom, shake_type
+ // nbufmax = largest buffer needed to hold info from any proc
+
+ nbuf = 0;
+ for (i = 0; i < nlocal; i++) {
+ if (shake_flag[i] == 0) continue;
+ for (j = 0; j < npartner[i]; j++) {
+ if (partner_shake[i][j] == 0) continue;
+ m = atom->map(partner_tag[i][j]);
+ if (m >= 0 && m < nlocal) {
+ shake_flag[m] = shake_flag[i];
+ shake_atom[m][0] = shake_atom[i][0];
+ shake_atom[m][1] = shake_atom[i][1];
+ shake_atom[m][2] = shake_atom[i][2];
+ shake_atom[m][3] = shake_atom[i][3];
+ shake_atom[m][4] = shake_atom[i][4];
+ shake_type[m][0] = shake_type[i][0];
+ shake_type[m][1] = shake_type[i][1];
+ shake_type[m][2] = shake_type[i][2];
+ shake_type[m][3] = shake_type[i][3];
+ } else nbuf += 11;
+ }
+ }
+
+ memory->create(buf,nbuf,"filter/corotate:buf");
+
+ // fill buffer with info
+
+ size = 0;
+ for (i = 0; i < nlocal; i++) {
+ if (shake_flag[i] == 0) continue;
+ for (j = 0; j < npartner[i]; j++) {
+ if (partner_shake[i][j] == 0) continue;
+ m = atom->map(partner_tag[i][j]);
+ if (m < 0 || m >= nlocal) {
+ buf[size] = partner_tag[i][j];
+ buf[size+1] = shake_flag[i];
+ buf[size+2] = shake_atom[i][0];
+ buf[size+3] = shake_atom[i][1];
+ buf[size+4] = shake_atom[i][2];
+ buf[size+5] = shake_atom[i][3];
+ buf[size+6] = shake_atom[i][4];
+ buf[size+7] = shake_type[i][0];
+ buf[size+8] = shake_type[i][1];
+ buf[size+9] = shake_type[i][2];
+ buf[size+10] = shake_type[i][3];
+ size += 11;
+ }
+ }
+ }
+
+ // cycle buffer around ring of procs back to self
+
+ fsptr = this;
+ comm->ring(size,sizeof(tagint),buf,3,ring_shake,NULL);
+
+ memory->destroy(buf);
+
+ // -----------------------------------------------------
+ // free local memory
+ // -----------------------------------------------------
+
+ memory->destroy(npartner);
+ memory->destroy(nshake);
+ memory->destroy(partner_tag);
+ memory->destroy(partner_mask);
+ memory->destroy(partner_type);
+ memory->destroy(partner_massflag);
+ memory->destroy(partner_bondtype);
+ memory->destroy(partner_shake);
+ memory->destroy(partner_nshake);
+
+ // -----------------------------------------------------
+ // print info on SHAKE clusters
+ // -----------------------------------------------------
+
+ int count1,count2,count3,count4,count5;
+ count1 = count2 = count3 = count4 = count5 = 0;
+ for (i = 0; i < nlocal; i++) {
+ if (shake_flag[i] == 1) count1++;
+ else if (shake_flag[i] == 2) count2++;
+ else if (shake_flag[i] == 3) count3++;
+ else if (shake_flag[i] == 4) count4++;
+ else if (shake_flag[i] == 5) count5++;
+ }
+
+ int tmp;
+ tmp = count1;
+ MPI_Allreduce(&tmp,&count1,1,MPI_INT,MPI_SUM,world);
+ tmp = count2;
+ MPI_Allreduce(&tmp,&count2,1,MPI_INT,MPI_SUM,world);
+ tmp = count3;
+ MPI_Allreduce(&tmp,&count3,1,MPI_INT,MPI_SUM,world);
+ tmp = count4;
+ MPI_Allreduce(&tmp,&count4,1,MPI_INT,MPI_SUM,world);
+ tmp = count5;
+ MPI_Allreduce(&tmp,&count5,1,MPI_INT,MPI_SUM,world);
+
+ if (me == 0) {
+ if (screen) {
+ fprintf(screen," %d = # of size 2 clusters\n",count2/2);
+ fprintf(screen," %d = # of size 3 clusters\n",count3/3);
+ fprintf(screen," %d = # of size 4 clusters\n",count4/4);
+ fprintf(screen," %d = # of size 5 clusters\n",count5/5);
+ fprintf(screen," %d = # of frozen angles\n",count1/3);
+ }
+ if (logfile) {
+ fprintf(logfile," %d = # of size 2 clusters\n",count2/2);
+ fprintf(logfile," %d = # of size 3 clusters\n",count3/3);
+ fprintf(logfile," %d = # of size 4 clusters\n",count4/4);
+ fprintf(logfile," %d = # of size 5 clusters\n",count5/5);
+ fprintf(logfile," %d = # of frozen angles\n",count1/3);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * when receive buffer, scan bond partner IDs for atoms I own
+ * if I own partner:
+ * fill in mask and type and massflag
+ * search for bond with 1st atom and fill in bondtype
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::ring_bonds(int ndatum, char *cbuf)
+{
+ Atom *atom = fsptr->atom;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *mask = atom->mask;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int nmass = fsptr->nmass;
+
+ tagint *buf = (tagint *) cbuf;
+ int m,n;
+ double massone;
+
+ for (int i = 0; i < ndatum; i += 6) {
+ m = atom->map(buf[i+1]);
+ if (m >= 0 && m < nlocal) {
+ buf[i+2] = mask[m];
+ buf[i+3] = type[m];
+ if (nmass) {
+ if (rmass) massone = rmass[m];
+ else massone = mass[type[m]];
+ buf[i+4] = fsptr->masscheck(massone);
+ }
+ if (buf[i+5] == 0) {
+ n = fsptr->bondtype_findset(m,buf[i],buf[i+1],0);
+ if (n) buf[i+5] = n;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * when receive buffer, scan bond partner IDs for atoms I own
+ * if I own partner, fill in nshake value
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::ring_nshake(int ndatum, char *cbuf)
+{
+ Atom *atom = fsptr->atom;
+ int nlocal = atom->nlocal;
+
+ int *nshake = fsptr->nshake;
+
+ tagint *buf = (tagint *) cbuf;
+ int m;
+
+ for (int i = 0; i < ndatum; i += 3) {
+ m = atom->map(buf[i+1]);
+ if (m >= 0 && m < nlocal) buf[i+2] = nshake[m];
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * when receive buffer, scan bond partner IDs for atoms I own
+ * if I own partner, fill in nshake value
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::ring_shake(int ndatum, char *cbuf)
+{
+ Atom *atom = fsptr->atom;
+ int nlocal = atom->nlocal;
+
+ int *shake_flag = fsptr->shake_flag;
+ tagint **shake_atom = fsptr->shake_atom;
+ int **shake_type = fsptr->shake_type;
+
+ tagint *buf = (tagint *) cbuf;
+ int m;
+
+ for (int i = 0; i < ndatum; i += 11) {
+ m = atom->map(buf[i]);
+ if (m >= 0 && m < nlocal) {
+ shake_flag[m] = buf[i+1];
+ shake_atom[m][0] = buf[i+2];
+ shake_atom[m][1] = buf[i+3];
+ shake_atom[m][2] = buf[i+4];
+ shake_atom[m][3] = buf[i+5];
+ shake_atom[m][4] = buf[i+6];
+ shake_type[m][0] = buf[i+7];
+ shake_type[m][1] = buf[i+8];
+ shake_type[m][2] = buf[i+9];
+ shake_type[m][3] = buf[i+10];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * check if massone is within MASSDELTA of any mass in mass_list
+ * return 1 if yes, 0 if not
+ * ------------------------------------------------------------------------- */
+
+int FixFilterCorotate::masscheck(double massone)
+{
+ for (int i = 0; i < nmass; i++) {
+ if (fabs(mass_list[i]-massone) <= MASSDELTA) return 1;
+ }
+ return 0;
+}
+
+/* --------------------------------------------------------------------------
+ * filter one cluster of arbitrary size
+ * ---------------------------------------------------------------------------*/
+
+void FixFilterCorotate::general_cluster(int index, int index_in_list)
+{
+ //index: shake index, index_in_list: corresponding index in list
+ //get q0, nselect:
+
+ double *q0 = clist_q0[index_in_list];
+ int nselect1 = clist_nselect1[index_in_list];
+ int nselect2 = clist_nselect2[index_in_list];
+ int *select1 = clist_select1[index_in_list];
+ int *select2 = clist_select2[index_in_list];
+
+ int N = shake_flag[index]; //number of atoms in cluster
+ if (N == 1) N = 3; //angle cluster
+
+ double**x = atom->x;
+ double norm1, norm2, norm3;
+
+ int* list_cluster = new int[N]; // contains local IDs of cluster atoms,
+ // 0 = center
+ double* m = new double[N]; //contains local mass
+ double *r = new double[N]; //contains r[i] = 1/||del[i]||
+ double** del = new double*[N]; //contains del[i] = x_i-x_0
+ for (int i = 0; i<N; i++)
+ del[i] = new double[3];
+
+ for (int i = 0; i < N; i++) {
+ list_cluster[i] = atom->map(shake_atom[index][i]);
+ m[i] = atom->mass[atom->type[list_cluster[i]]];
+ }
+
+ //%CALC r_i:
+ for (int i = 1; i < N; i++) {
+ del[i][0] = x[list_cluster[i]][0] - x[list_cluster[0]][0];
+ del[i][1] = x[list_cluster[i]][1] - x[list_cluster[0]][1];
+ del[i][2] = x[list_cluster[i]][2] - x[list_cluster[0]][2];
+ domain->minimum_image(del[i]);
+ r[i] = 1.0/sqrt(del[i][0]*del[i][0]+del[i][1]*del[i][1]+
+ del[i][2]*del[i][2]);
+ }
+ //special case i=0: need del[0] for compact notation of array_atom later...
+ del[0][0] = del[0][1] = del[0][2] = r[0] = 0.0;
+
+ //calc n1:
+ n1[0] = n1[1] = n1[2] = 0.0;
+
+ int k;
+ for (int i = 0; i < nselect1; i++) {
+ k = select1[i];
+ n1[0] += del[k][0]*r[k];
+ n1[1] += del[k][1]*r[k];
+ n1[2] += del[k][2]*r[k];
+ }
+ norm1 = 1.0/sqrt(n1[0]*n1[0]+n1[1]*n1[1]+n1[2]*n1[2]);
+
+ n1[0] *= norm1;
+ n1[1] *= norm1;
+ n1[2] *= norm1;
+
+ //calc n2:
+ n2[0] = n2[1] = n2[2] = 0.0;
+
+ for (int i = 0; i < nselect2; i++) {
+ k = select2[i];
+ n2[0] += del[k][0]*r[k];
+ n2[1] += del[k][1]*r[k];
+ n2[2] += del[k][2]*r[k];
+ }
+ if (!nselect2) //cluster of size 2, has only one direction
+ n2[0] = n2[1] = n2[2] = 1.0;
+
+ double alpha = n2[0]*n1[0] + n2[1]*n1[1] + n2[2]*n1[2];
+
+ n2[0] -= alpha*n1[0];
+ n2[1] -= alpha*n1[1];
+ n2[2] -= alpha*n1[2];
+
+ norm2 = 1.0/sqrt(n2[0]*n2[0]+n2[1]*n2[1]+n2[2]*n2[2]);
+
+ n2[0] *= norm2;
+ n2[1] *= norm2;
+ n2[2] *= norm2;
+
+ n3[0] = n1[1]*n2[2] - n1[2]*n2[1];
+ n3[1] = n1[2]*n2[0] - n1[0]*n2[2];
+ n3[2] = n1[0]*n2[1] - n1[1]*n2[0];
+
+ norm3 = 1.0/sqrt(n3[0]*n3[0]+n3[1]*n3[1]+n3[2]*n3[2]);
+
+ n3[0] *= norm3;
+ n3[1] *= norm3;
+ n3[2] *= norm3;
+
+ //%x_filter:
+ for (int i = 0; i < N; i++) {
+ k = list_cluster[i];
+ array_atom[k][0] = x[k][0]+q0[3*i]*n1[0]+q0[3*i+1]*n2[0]+q0[3*i+2]*n3[0];
+ array_atom[k][1] = x[k][1]+q0[3*i]*n1[1]+q0[3*i+1]*n2[1]+q0[3*i+2]*n3[1];
+ array_atom[k][2] = x[k][2]+q0[3*i]*n1[2]+q0[3*i+1]*n2[2]+q0[3*i+2]*n3[2];
+ }
+
+ double m_all = 0.0;
+ for (int i = 0; i<N; i++)
+ m_all += m[i];
+
+ //%x+X_center
+
+ for (int i = 0; i<N; i++) {
+ k = list_cluster[i];
+ for (int j = 0; j < N; j++) {
+ array_atom[k][0] += m[j]/m_all*(del[j][0]-del[i][0]);
+ array_atom[k][1] += m[j]/m_all*(del[j][1]-del[i][1]);
+ array_atom[k][2] += m[j]/m_all*(del[j][2]-del[i][2]);
+ }
+ }
+
+ //derivative:
+ //dn1dx:
+ double sum1[3][3*N];
+ for (int i=0; i<3; i++)
+ for (int j=0; j<3*N; j++)
+ sum1[i][j] = 0;
+
+ double I3mn1n1T[3][3]; //(I_3 - n1n1T)
+ for (int i=0; i<3; i++) {
+ for (int j=0; j<3; j++)
+ I3mn1n1T[i][j] = -n1[i]*n1[j];
+ I3mn1n1T[i][i] += 1.0;
+ }
+
+ // sum1 part of dn1dx:
+
+ for (int l = 0; l < nselect1; l++) {
+ k = select1[l];
+ for (int i=0; i<3; i++) {
+ for (int j=0; j<3; j++) {
+ double help = del[k][i]*del[k][j]*r[k]*r[k]*r[k];
+ sum1[i][j+3*k] -= help;
+ sum1[i][j] += help;
+ }
+ sum1[i][i+3*k] += r[k];
+ sum1[i][i] -= r[k];
+ }
+ }
+
+ //dn1dx = norm1 * I3mn1n1T * sum1
+
+ for (int i=0; i<3; i++) {
+ for (int j=0; j<3*N; j++) {
+ double sum = 0;
+ for (int l = 0; l<3; l++)
+ sum += I3mn1n1T[i][l]*sum1[l][j];
+ dn1dx[i][j] = norm1*sum;
+ }
+ }
+
+ //dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
+
+ double sum2[3][3*N];
+ for (int i=0; i<3; i++)
+ for (int j=0; j<3*N; j++)
+ sum2[i][j] = 0;
+
+ double I3mn2n2T[3][3]; //(I_3 - n2n2T)
+ for (int i=0; i<3; i++) {
+ for (int j=0; j<3; j++)
+ I3mn2n2T[i][j] = -n2[i]*n2[j];
+ I3mn2n2T[i][i] += 1.0;
+ }
+
+ // sum2 part of dn1dx:
+
+ for (int l = 0; l < nselect2; l++) {
+ k = select2[l];
+ for (int i=0; i<3; i++) {
+ for (int j=0; j<3; j++) {
+ double help = del[k][i]*del[k][j]*r[k]*r[k]*r[k];
+ sum2[i][j+3*k] -= help;
+ sum2[i][j] += help;
+ }
+ sum2[i][i+3*k] += r[k];
+ sum2[i][i] -= r[k];
+ }
+ }
+
+ //prefactor:
+
+ double rkn1pn1rk[3][3];
+ double rk[3]; rk[0] = rk[1] = rk[2] = 0.0;
+
+ for (int i = 0; i < nselect2; i++) {
+ k = select2[i];
+ rk[0] += del[k][0]*r[k];
+ rk[1] += del[k][1]*r[k];
+ rk[2] += del[k][2]*r[k];
+ }
+
+ //rkn1pn1rk = rkT*n1*I3 + n1*rkT
+
+ double scalar = rk[0]*n1[0]+rk[1]*n1[1]+rk[2]*n1[2];
+ for (int i=0; i<3; i++) {
+ for (int j=0; j<3; j++)
+ rkn1pn1rk[i][j] = n1[i]*rk[j];
+ rkn1pn1rk[i][i] += scalar;
+ }
+
+ //dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
+ //sum3 = (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
+
+ double sum3[3][3*N];
+ for (int i=0; i<3; i++)
+ for (int j=0; j<3*N; j++) {
+ double sum = 0;
+ for (int l = 0; l<3; l++)
+ sum += I3mn1n1T[i][l]*sum2[l][j] - rkn1pn1rk[i][l]*dn1dx[l][j];
+ sum3[i][j] = sum;
+ }
+
+ //dn2dx = norm2 * I3mn2n2T * sum3
+ for (int i=0; i<3; i++)
+ for (int j=0; j<3*N; j++) {
+ double sum = 0;
+ for (int l = 0; l<3; l++)
+ sum += I3mn2n2T[i][l]*sum3[l][j];
+ dn2dx[i][j] = norm2*sum;
+ }
+
+ //dn3dx = norm3 * I3mn3n3T * cross
+ double I3mn3n3T[3][3]; //(I_3 - n3n3T)
+ for (int i=0; i<3; i++) {
+ for (int j=0; j<3; j++)
+ I3mn3n3T[i][j] = -n3[i]*n3[j];
+ I3mn3n3T[i][i] += 1.0;
+ }
+
+ double cross[3][3*N];
+
+ for (int j=0; j<3*N; j++) {
+ cross[0][j] = dn1dx[1][j]*n2[2] -dn1dx[2][j]*n2[1] +
+ n1[1]*dn2dx[2][j]-n1[2]*dn2dx[1][j];
+ cross[1][j] = dn1dx[2][j]*n2[0] -dn1dx[0][j]*n2[2] +
+ n1[2]*dn2dx[0][j]-n1[0]*dn2dx[2][j];
+ cross[2][j] = dn1dx[0][j]*n2[1] -dn1dx[1][j]*n2[0] +
+ n1[0]*dn2dx[1][j]-n1[1]*dn2dx[0][j];
+ }
+
+ for (int i=0; i<3; i++)
+ for (int j=0; j<3*N; j++) {
+ double sum = 0;
+ for (int l = 0; l<3; l++)
+ sum += I3mn3n3T[i][l]*cross[l][j];
+ dn3dx[i][j] = norm3*sum;
+ }
+
+ for (int l=0; l<N; l++)
+ for (int i=0; i<3; i++)
+ for (int j=0; j<3*N; j++)
+ help2[i+3*l][j] = q0[3*l]*dn1dx[i][j] + q0[3*l+1]*dn2dx[i][j] +
+ q0[3*l+2]*dn3dx[i][j];
+
+ for (int j=0; j<N; j++)
+ for (int l=0; l<N; l++)
+ for (int i=0; i<3; i++)
+ help2[i+3*l][i+3*j] += m[j]/m_all;
+
+ //need transposed of help2:
+ for (int ii = 0; ii < 3*N; ii++)
+ for (int jj = 0; jj < 3*N; jj++)
+ clist_derv[index_in_list][ii][jj] = help2[jj][ii];
+
+ //free memory
+ delete [] list_cluster;
+ delete [] m;
+ delete [] r;
+ for (int i = 0; i<N; i++)
+ delete [] del[i];
+ delete [] del;
+}
+
+int FixFilterCorotate::pack_forward_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double**f = atom->f;
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+
+ buf[m++] = f[j][0];
+ buf[m++] = f[j][1];
+ buf[m++] = f[j][2];
+ }
+ return m;
+}
+
+void FixFilterCorotate::unpack_forward_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+ double **f = atom->f;
+ m = 0;
+ last = first + n;
+
+ for (i = first; i < last; i++)
+ {
+ f[i][0] = buf[m++];
+ f[i][1] = buf[m++];
+ f[i][2] = buf[m++];
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * find a bond between global atom IDs n1 and n2 stored with local atom i
+ * if find it:
+ * if setflag = 0, return bond type
+ * if setflag = -1/1, set bond type to negative/positive and return 0
+ * if do not find it, return 0
+ * ------------------------------------------------------------------------- */
+
+int FixFilterCorotate::bondtype_findset(int i, tagint n1, tagint n2,
+ int setflag)
+{
+ int m,nbonds;
+
+ tagint *tag = atom->tag;
+ tagint **bond_atom = atom->bond_atom;
+ nbonds = atom->num_bond[i];
+
+ for (m = 0; m < nbonds; m++) {
+ if (n1 == tag[i] && n2 == bond_atom[i][m]) break;
+ if (n1 == bond_atom[i][m] && n2 == tag[i]) break;
+ }
+
+ if (m < nbonds) {
+ if (setflag == 0)
+ return atom->bond_type[i][m];
+
+ if ((setflag < 0 && atom->bond_type[i][m] > 0) ||
+ (setflag > 0 && atom->bond_type[i][m] < 0))
+ atom->bond_type[i][m] = -atom->bond_type[i][m];
+
+ }
+
+ return 0;
+}
+
+/* ----------------------------------------------------------------------
+ * find an angle with global end atom IDs n1 and n2 stored with local atom i
+ * if find it:
+ * if setflag = 0, return angle type
+ * if setflag = -1/1, set angle type to negative/positive and return 0
+ * if do not find it, return 0
+ * ------------------------------------------------------------------------- */
+
+int FixFilterCorotate::angletype_findset(int i, tagint n1, tagint n2,
+ int setflag)
+{
+ int m,nangles;
+
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom3 = atom->angle_atom3;
+ nangles = atom->num_angle[i];
+
+ for (m = 0; m < nangles; m++) {
+ if (n1 == angle_atom1[i][m] && n2 == angle_atom3[i][m]) break;
+ if (n1 == angle_atom3[i][m] && n2 == angle_atom1[i][m]) break;
+ }
+
+ if (m < nangles) {
+ if (setflag == 0) {
+ return atom->angle_type[i][m];
+ }
+
+ if ((setflag < 0 && atom->angle_type[i][m] > 0) ||
+ (setflag > 0 && atom->angle_type[i][m] < 0))
+ atom->angle_type[i][m] = -atom->angle_type[i][m];
+ }
+
+ return 0;
+}
+
+/* ----------------------------------------------------------------------
+ * allocate local atom-based arrays
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::grow_arrays(int nmax)
+{
+ memory->grow(array_atom,nmax,3,"FilterCorotate:peratomarray");
+ memory->grow(shake_flag,nmax,"FilterCorotate::shake_flag");
+ memory->grow(shake_atom,nmax,5,"FilterCorotate::shake_atom");
+ memory->grow(shake_type,nmax,4,"FilterCorotate::shake_type");
+}
+
+/* ----------------------------------------------------------------------
+ * memory usage of local atom-based arrays
+ * ------------------------------------------------------------------------- */
+
+double FixFilterCorotate::memory_usage()
+{
+ double bytes = 0;
+ //GROW:
+ bytes += 3*sizeof(double) + 5*sizeof(tagint) + 5*sizeof(int);
+ //clist
+ bytes += 13*atom->nlocal*sizeof(int);
+ bytes += 15*16*nlocal*sizeof(double);
+
+ //fixed:
+ int nb = atom->nbondtypes+1;
+ int na = atom->nangletypes+1;
+ int nt = atom->ntypes+1;
+ bytes += (nb+na+nt)*sizeof(int);
+ bytes += (nt-1+nb+na+15*15+18+10*15)*sizeof(double);
+
+ return bytes;
+}
+
+
+/* ----------------------------------------------------------------------
+ * copy values within local atom-based arrays
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::copy_arrays(int i, int j, int delflag)
+{
+ int flag = shake_flag[j] = shake_flag[i];
+ if (flag == 1) {
+ shake_atom[j][0] = shake_atom[i][0];
+ shake_atom[j][1] = shake_atom[i][1];
+ shake_atom[j][2] = shake_atom[i][2];
+ shake_type[j][0] = shake_type[i][0];
+ shake_type[j][1] = shake_type[i][1];
+ shake_type[j][2] = shake_type[i][2];
+ } else if (flag == 2) {
+ shake_atom[j][0] = shake_atom[i][0];
+ shake_atom[j][1] = shake_atom[i][1];
+ shake_type[j][0] = shake_type[i][0];
+ } else if (flag == 3) {
+ shake_atom[j][0] = shake_atom[i][0];
+ shake_atom[j][1] = shake_atom[i][1];
+ shake_atom[j][2] = shake_atom[i][2];
+ shake_type[j][0] = shake_type[i][0];
+ shake_type[j][1] = shake_type[i][1];
+ shake_type[j][2] = shake_type[i][2];
+ } else if (flag == 4) {
+ shake_atom[j][0] = shake_atom[i][0];
+ shake_atom[j][1] = shake_atom[i][1];
+ shake_atom[j][2] = shake_atom[i][2];
+ shake_atom[j][3] = shake_atom[i][3];
+ shake_type[j][0] = shake_type[i][0];
+ shake_type[j][1] = shake_type[i][1];
+ shake_type[j][2] = shake_type[i][2];
+ } else if (flag == 5) {
+ shake_atom[j][0] = shake_atom[i][0];
+ shake_atom[j][1] = shake_atom[i][1];
+ shake_atom[j][2] = shake_atom[i][2];
+ shake_atom[j][3] = shake_atom[i][3];
+ shake_atom[j][4] = shake_atom[i][4];
+ shake_type[j][0] = shake_type[i][0];
+ shake_type[j][1] = shake_type[i][1];
+ shake_type[j][2] = shake_type[i][2];
+ shake_type[j][3] = shake_type[i][3];
+ }
+}
+
+/* ----------------------------------------------------------------------
+ * initialize one atom's array values, called when atom is created
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::set_arrays(int i)
+{
+ shake_flag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+ * update one atom's array values
+ * called when molecule is created from fix gcmc
+ * ------------------------------------------------------------------------- */
+
+void FixFilterCorotate::update_arrays(int i, int atom_offset)
+{
+ int flag = shake_flag[i];
+
+ if (flag == 1) {
+ shake_atom[i][0] += atom_offset;
+ shake_atom[i][1] += atom_offset;
+ shake_atom[i][2] += atom_offset;
+ } else if (flag == 2) {
+ shake_atom[i][0] += atom_offset;
+ shake_atom[i][1] += atom_offset;
+ } else if (flag == 3) {
+ shake_atom[i][0] += atom_offset;
+ shake_atom[i][1] += atom_offset;
+ shake_atom[i][2] += atom_offset;
+ } else if (flag == 4) {
+ shake_atom[i][0] += atom_offset;
+ shake_atom[i][1] += atom_offset;
+ shake_atom[i][2] += atom_offset;
+ shake_atom[i][3] += atom_offset;
+ } else if (flag == 5) {
+ shake_atom[i][0] += atom_offset;
+ shake_atom[i][1] += atom_offset;
+ shake_atom[i][2] += atom_offset;
+ shake_atom[i][3] += atom_offset;
+ shake_atom[i][4] += atom_offset;
+ }
+}
+
+
+/* ----------------------------------------------------------------------
+ * pack values in local atom-based arrays for exchange with another proc
+ * ------------------------------------------------------------------------- */
+
+int FixFilterCorotate::pack_exchange(int i, double *buf)
+{
+ int m = 0;
+ buf[m++] = shake_flag[i];
+ int flag = shake_flag[i];
+ if (flag == 1) {
+ buf[m++] = shake_atom[i][0];
+ buf[m++] = shake_atom[i][1];
+ buf[m++] = shake_atom[i][2];
+ buf[m++] = shake_type[i][0];
+ buf[m++] = shake_type[i][1];
+ buf[m++] = shake_type[i][2];
+ } else if (flag == 2) {
+ buf[m++] = shake_atom[i][0];
+ buf[m++] = shake_atom[i][1];
+ buf[m++] = shake_type[i][0];
+ } else if (flag == 3) {
+ buf[m++] = shake_atom[i][0];
+ buf[m++] = shake_atom[i][1];
+ buf[m++] = shake_atom[i][2];
+ buf[m++] = shake_type[i][0];
+ buf[m++] = shake_type[i][1];
+ buf[m++] = shake_type[i][2];
+ } else if (flag == 4) {
+ buf[m++] = shake_atom[i][0];
+ buf[m++] = shake_atom[i][1];
+ buf[m++] = shake_atom[i][2];
+ buf[m++] = shake_atom[i][3];
+ buf[m++] = shake_type[i][0];
+ buf[m++] = shake_type[i][1];
+ buf[m++] = shake_type[i][2];
+ } else if (flag == 5) {
+ buf[m++] = shake_atom[i][0];
+ buf[m++] = shake_atom[i][1];
+ buf[m++] = shake_atom[i][2];
+ buf[m++] = shake_atom[i][3];
+ buf[m++] = shake_atom[i][4];
+ buf[m++] = shake_type[i][0];
+ buf[m++] = shake_type[i][1];
+ buf[m++] = shake_type[i][2];
+ buf[m++] = shake_type[i][3];
+ }
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ * unpack values in local atom-based arrays from exchange with another proc
+ * ------------------------------------------------------------------------- */
+
+int FixFilterCorotate::unpack_exchange(int nlocal, double *buf)
+{
+ int m = 0;
+ int flag = shake_flag[nlocal] = static_cast<int> (buf[m++]);
+ if (flag == 1) {
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
+ shake_type[nlocal][0] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][1] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][2] = static_cast<int> (buf[m++]);
+ } else if (flag == 2) {
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
+ shake_type[nlocal][0] = static_cast<int> (buf[m++]);
+ } else if (flag == 3) {
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
+ shake_type[nlocal][0] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][1] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][2] = static_cast<int> (buf[m++]);
+ } else if (flag == 4) {
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][3] = static_cast<tagint> (buf[m++]);
+ shake_type[nlocal][0] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][1] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][2] = static_cast<int> (buf[m++]);
+ } else if (flag == 5) {
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][3] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][4] = static_cast<tagint> (buf[m++]);
+ shake_type[nlocal][0] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][1] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][2] = static_cast<int> (buf[m++]);
+ shake_type[nlocal][3] = static_cast<int> (buf[m++]);
+ }
+ return m;
+}
diff --git a/src/USER-MISC/fix_filter_corotate.h b/src/USER-MISC/fix_filter_corotate.h
new file mode 100644
index 0000000000000000000000000000000000000000..47accfedd3d2cf08e94d7cabe33fafa0cc20c54c
--- /dev/null
+++ b/src/USER-MISC/fix_filter_corotate.h
@@ -0,0 +1,139 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Lukas Fath (KIT)
+ some subroutines are from fix_shake.cpp
+ ------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(filter/corotate,FixFilterCorotate)
+
+#else
+
+#ifndef LMP_FIX_FILTER_COROTATE_H
+#define LMP_FIX_FILTER_COROTATE_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS
+{
+
+ class FixFilterCorotate : public Fix
+ {
+ public:
+
+ FixFilterCorotate(class LAMMPS *, int, char **);
+ ~FixFilterCorotate();
+ void setup(int);
+ void setup_pre_neighbor();
+ void pre_neighbor();
+ void setup_pre_force_respa(int,int);
+// void setup_post_force_respa(int,int);
+ void pre_force_respa(int, int, int);
+ void post_force_respa(int, int, int);
+
+ void init();
+ int setmask();
+
+ double compute_array(int,int);
+
+ int pack_forward_comm(int, int *, double *, int, int *);
+ void unpack_forward_comm(int, int, double *);
+ void grow_arrays(int );
+ double memory_usage();
+
+ void copy_arrays(int, int, int);
+ void set_arrays(int);
+ void update_arrays(int, int);
+
+ int pack_exchange(int, double *);
+ int unpack_exchange(int, double *);
+
+ protected:
+
+ int me,nprocs;
+
+ int flevel; //filtered respa level
+
+ double **help2; //temp derivative
+ double **x_store; //temp for atom->x
+ double *g; //temp for derivative
+
+ double*n1,*n2,*n3, *del1, *del2,*del3;
+
+ double**dn1dx,**dn2dx,**dn3dx;
+
+ int *bond_flag,*angle_flag; // bond/angle types to constrain
+ int *type_flag; // constrain bonds to these types
+ double *mass_list; // constrain bonds to these masses
+ int nmass; // # of masses in mass_list
+
+ int molecular; // copy of atom->molecular
+ double *bond_distance,*angle_distance; // constraint distances
+
+ int nlevels_respa; // copies of needed rRESPA variables
+
+ double **x,**v,**f; // local ptrs to atom class quantities
+ double *mass,*rmass;
+ int *type;
+ int nlocal;
+ // atom-based arrays
+ int *shake_flag; // 0 if atom not in SHAKE cluster
+ // 1 = size 3 angle cluster
+ // 2,3,4 = size of bond-only cluster
+ tagint **shake_atom; // global IDs of atoms in cluster
+ // central atom is 1st
+ // lowest global ID is 1st for size 2
+ int **shake_type; // bondtype of each bond in cluster
+ // for angle cluster, 3rd value
+ // is angletype
+ int *nshake; // count
+
+ int *list; // list of clusters to SHAKE
+ int nlist,maxlist; // size and max-size of list
+ double ***clist_derv; //stores derivative
+ double **clist_q0; //stores reference config
+ int *clist_nselect1, *clist_nselect2; //stores length of each selec. list
+ int **clist_select1, **clist_select2; //stores selection lists
+
+ void find_clusters();
+ int masscheck(double);
+
+ void filter_inner();
+ void filter_outer();
+
+ void general_cluster(int,int);
+
+ void stats();
+ int bondtype_findset(int, tagint, tagint, int);
+ int angletype_findset(int, tagint, tagint, int);
+
+ // static variable for ring communication callback to access class data
+ // callback functions for ring communication
+
+ static FixFilterCorotate *fsptr;
+ static void ring_bonds(int, char *);
+ static void ring_nshake(int, char *);
+ static void ring_shake(int, char *);
+
+ int sgn(double val) {
+ return (0 < val) - (val < 0);
+ };
+ };
+
+}
+
+#endif
+#endif