type labels for nylon_melt example
This commit is contained in:
Jacob Gissinger
@ -18,14 +18,19 @@ dihedral_style class2
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improper_style class2
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read_data large_nylon_melt.data.gz
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read_data large_nylon_melt.data.gz &
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extra/bond/per/atom 5 &
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extra/angle/per/atom 15 &
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extra/dihedral/per/atom 15 &
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extra/improper/per/atom 25 &
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extra/special/per/atom 25
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velocity all create 800.0 4928459 dist gaussian
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molecule mol1 rxn1_stp1_unreacted.data_template
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molecule mol2 rxn1_stp1_reacted.data_template
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molecule mol3 rxn1_stp2_unreacted.data_template
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molecule mol4 rxn1_stp2_reacted.data_template
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molecule mol1 rxn1_stp1_unreacted.molecule_template
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molecule mol2 rxn1_stp1_reacted.molecule_template
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molecule mol3 rxn1_stp2_unreacted.molecule_template
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molecule mol4 rxn1_stp2_reacted.molecule_template
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thermo 50
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Binary file not shown.
@ -1,175 +0,0 @@
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LAMMPS (20 Apr 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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using 1 OpenMP thread(s) per MPI task
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# 35,000 atom nylon melt example
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units real
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boundary p p p
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atom_style full
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kspace_style pppm 1.0e-4
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pair_style lj/class2/coul/long 8.5
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angle_style class2
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bond_style class2
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dihedral_style class2
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improper_style class2
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read_data large_nylon_melt.data.gz
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orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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35200 atoms
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reading velocities ...
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35200 velocities
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scanning bonds ...
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9 = max bonds/atom
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scanning angles ...
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21 = max angles/atom
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scanning dihedrals ...
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31 = max dihedrals/atom
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scanning impropers ...
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29 = max impropers/atom
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reading bonds ...
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33600 bonds
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reading angles ...
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59200 angles
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reading dihedrals ...
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80000 dihedrals
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reading impropers ...
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35200 impropers
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4 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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12 = max # of 1-4 neighbors
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41 = max # of special neighbors
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velocity all create 800.0 4928459 dist gaussian
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molecule mol1 rxn1_stp1_unreacted.data_template
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Read molecule mol1:
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18 atoms with max type 8
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16 bonds with max type 12
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25 angles with max type 24
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23 dihedrals with max type 33
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14 impropers with max type 9
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molecule mol2 rxn1_stp1_reacted.data_template
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Read molecule mol2:
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18 atoms with max type 9
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17 bonds with max type 11
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31 angles with max type 23
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39 dihedrals with max type 30
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20 impropers with max type 1
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molecule mol3 rxn1_stp2_unreacted.data_template
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Read molecule mol3:
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15 atoms with max type 9
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14 bonds with max type 11
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25 angles with max type 23
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30 dihedrals with max type 30
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16 impropers with max type 1
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molecule mol4 rxn1_stp2_reacted.data_template
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Read molecule mol4:
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15 atoms with max type 11
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13 bonds with max type 13
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19 angles with max type 25
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16 dihedrals with max type 29
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10 impropers with max type 11
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thermo 50
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# dump 1 all xyz 100 test_vis.xyz
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fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
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WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
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WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
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dynamic group bond_react_MASTER_group defined
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dynamic group statted_grp defined
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dynamic group bond_react_MASTER_group defined
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dynamic group statted_grp defined
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# stable at 800K
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fix 1 statted_grp nvt temp 800 800 100
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# in order to customize behavior of reacting atoms,
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# you can use the internally created 'bond_react_MASTER_group', like so:
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# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
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thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
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# restart 100 restart1 restart2
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run 200
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.20765
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grid = 18 18 18
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0333156
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estimated relative force accuracy = 0.000100329
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using double precision FFTs
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3d grid and FFT values/proc = 12167 5832
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.5
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ghost atom cutoff = 10.5
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binsize = 5.25, bins = 15 15 15
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/class2/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) fix bond/react, occasional, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
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Step Temp Press Density f_myrxns[1] f_myrxns[2]
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0 800 3666.3948 0.80366765 0 0
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50 673.95238 -9670.9169 0.80366765 31 0
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100 697.22819 -4624.0512 0.80366765 57 22
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150 723.60507 -17175.571 0.80366765 76 48
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200 736.71277 -12961.963 0.80366765 84 64
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Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
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Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
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99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45
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Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01
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Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07
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Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22
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Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40
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Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00
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Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81
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Other | | 0.04545 | | | 0.04
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Nlocal: 35200 ave 35200 max 35200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 38403 ave 38403 max 38403 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 6928101
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Ave neighs/atom = 196.821
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Ave special neighs/atom = 9.83727
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Neighbor list builds = 200
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Dangerous builds = 0
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# write_restart restart_longrun
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# write_data restart_longrun.data
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:01:43
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@ -1,175 +0,0 @@
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LAMMPS (20 Apr 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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using 1 OpenMP thread(s) per MPI task
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# 35,000 atom nylon melt example
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units real
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boundary p p p
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atom_style full
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kspace_style pppm 1.0e-4
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pair_style lj/class2/coul/long 8.5
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angle_style class2
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bond_style class2
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dihedral_style class2
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improper_style class2
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read_data large_nylon_melt.data.gz
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orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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35200 atoms
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reading velocities ...
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35200 velocities
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scanning bonds ...
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9 = max bonds/atom
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scanning angles ...
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21 = max angles/atom
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scanning dihedrals ...
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31 = max dihedrals/atom
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scanning impropers ...
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29 = max impropers/atom
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reading bonds ...
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33600 bonds
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reading angles ...
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59200 angles
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reading dihedrals ...
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80000 dihedrals
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reading impropers ...
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35200 impropers
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4 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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12 = max # of 1-4 neighbors
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41 = max # of special neighbors
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velocity all create 800.0 4928459 dist gaussian
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molecule mol1 rxn1_stp1_unreacted.data_template
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Read molecule mol1:
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18 atoms with max type 8
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16 bonds with max type 12
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25 angles with max type 24
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23 dihedrals with max type 33
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14 impropers with max type 9
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molecule mol2 rxn1_stp1_reacted.data_template
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Read molecule mol2:
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18 atoms with max type 9
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17 bonds with max type 11
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31 angles with max type 23
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39 dihedrals with max type 30
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20 impropers with max type 1
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molecule mol3 rxn1_stp2_unreacted.data_template
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Read molecule mol3:
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15 atoms with max type 9
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14 bonds with max type 11
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25 angles with max type 23
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30 dihedrals with max type 30
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16 impropers with max type 1
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molecule mol4 rxn1_stp2_reacted.data_template
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Read molecule mol4:
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15 atoms with max type 11
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13 bonds with max type 13
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19 angles with max type 25
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16 dihedrals with max type 29
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10 impropers with max type 11
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thermo 50
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# dump 1 all xyz 100 test_vis.xyz
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fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
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WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
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WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
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dynamic group bond_react_MASTER_group defined
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dynamic group statted_grp defined
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dynamic group bond_react_MASTER_group defined
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dynamic group statted_grp defined
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# stable at 800K
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fix 1 statted_grp nvt temp 800 800 100
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|
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# in order to customize behavior of reacting atoms,
|
||||
# you can use the internally created 'bond_react_MASTER_group', like so:
|
||||
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
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|
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thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
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||||
|
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# restart 100 restart1 restart2
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run 200
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PPPM initialization ...
|
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using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
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G vector (1/distance) = 0.20765
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grid = 18 18 18
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0333156
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estimated relative force accuracy = 0.000100329
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using double precision FFTs
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3d grid and FFT values/proc = 4508 1620
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.5
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ghost atom cutoff = 10.5
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binsize = 5.25, bins = 15 15 15
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/class2/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) fix bond/react, occasional, copy from (1)
|
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
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Step Temp Press Density f_myrxns[1] f_myrxns[2]
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0 800 3666.3948 0.80366765 0 0
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50 673.95238 -9670.9169 0.80366765 31 0
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100 697.22819 -4624.0512 0.80366765 57 22
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150 724.40407 -17166.729 0.80366765 76 49
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200 737.28582 -12968.224 0.80366765 84 65
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Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
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Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
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98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89
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Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31
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Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19
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Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68
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Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47
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Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00
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Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39
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Other | | 0.03995 | | | 0.08
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Nlocal: 8800 ave 8913 max 8652 min
|
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Nghost: 18366 ave 18461 max 18190 min
|
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
|
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Histogram: 1 0 1 0 0 0 0 0 0 2
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||||
|
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Total # of neighbors = 6928132
|
||||
Ave neighs/atom = 196.822
|
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Ave special neighs/atom = 9.83608
|
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Neighbor list builds = 200
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart restart_longrun
|
||||
# write_data restart_longrun.data
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:52
|
||||
@ -0,0 +1,150 @@
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LAMMPS (4 Nov 2022)
|
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Reading data file ...
|
||||
orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atom labelmap ...
|
||||
reading bond labelmap ...
|
||||
reading angle labelmap ...
|
||||
reading dihedral labelmap ...
|
||||
reading improper labelmap ...
|
||||
reading atoms ...
|
||||
35200 atoms
|
||||
reading velocities ...
|
||||
35200 velocities
|
||||
scanning bonds ...
|
||||
9 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
31 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
33600 bonds
|
||||
reading angles ...
|
||||
59200 angles
|
||||
reading dihedrals ...
|
||||
80000 dihedrals
|
||||
reading impropers ...
|
||||
35200 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
41 = max # of special neighbors
|
||||
special bonds CPU = 0.026 seconds
|
||||
read_data CPU = 0.937 seconds
|
||||
Read molecule template mol1:
|
||||
1 molecules
|
||||
0 fragments
|
||||
18 atoms with max type 8
|
||||
16 bonds with max type 12
|
||||
25 angles with max type 24
|
||||
23 dihedrals with max type 33
|
||||
2 impropers with max type 9
|
||||
Read molecule template mol2:
|
||||
1 molecules
|
||||
0 fragments
|
||||
18 atoms with max type 9
|
||||
17 bonds with max type 11
|
||||
31 angles with max type 23
|
||||
39 dihedrals with max type 30
|
||||
0 impropers with max type 0
|
||||
Read molecule template mol3:
|
||||
1 molecules
|
||||
0 fragments
|
||||
15 atoms with max type 9
|
||||
14 bonds with max type 11
|
||||
25 angles with max type 23
|
||||
30 dihedrals with max type 30
|
||||
0 impropers with max type 0
|
||||
Read molecule template mol4:
|
||||
1 molecules
|
||||
0 fragments
|
||||
15 atoms with max type 11
|
||||
13 bonds with max type 13
|
||||
19 angles with max type 25
|
||||
16 dihedrals with max type 29
|
||||
2 impropers with max type 11
|
||||
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
|
||||
The log file lists these citations in BibTeX format.
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20765034
|
||||
grid = 18 18 18
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.033315619
|
||||
estimated relative force accuracy = 0.000100329
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 12167 5832
|
||||
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 15 15 15
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 209.8 | 209.8 | 209.8 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 800 3666.3948 0.80366765 0 0
|
||||
50 673.94821 -9679.5038 0.80366765 31 0
|
||||
100 694.45718 -2104.8514 0.80366765 57 22
|
||||
150 716.53915 -12356.83 0.80366765 77 50
|
||||
200 723.33218 -1319.9666 0.80366765 84 67
|
||||
Loop time of 87.9809 on 1 procs for 200 steps with 35200 atoms
|
||||
|
||||
Performance: 0.196 ns/day, 122.196 hours/ns, 2.273 timesteps/s, 80.017 katom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 25.691 | 25.691 | 25.691 | 0.0 | 29.20
|
||||
Bond | 15.772 | 15.772 | 15.772 | 0.0 | 17.93
|
||||
Kspace | 4.611 | 4.611 | 4.611 | 0.0 | 5.24
|
||||
Neigh | 35.616 | 35.616 | 35.616 | 0.0 | 40.48
|
||||
Comm | 0.24971 | 0.24971 | 0.24971 | 0.0 | 0.28
|
||||
Output | 0.00098602 | 0.00098602 | 0.00098602 | 0.0 | 0.00
|
||||
Modify | 5.9596 | 5.9596 | 5.9596 | 0.0 | 6.77
|
||||
Other | | 0.08051 | | | 0.09
|
||||
|
||||
Nlocal: 35200 ave 35200 max 35200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 38403 ave 38403 max 38403 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6.92764e+06 ave 6.92764e+06 max 6.92764e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 6927635
|
||||
Ave neighs/atom = 196.80781
|
||||
Ave special neighs/atom = 9.8480114
|
||||
Neighbor list builds = 128
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:29
|
||||
@ -0,0 +1,151 @@
|
||||
LAMMPS (4 Nov 2022)
|
||||
WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:529)
|
||||
Reading data file ...
|
||||
orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atom labelmap ...
|
||||
reading bond labelmap ...
|
||||
reading angle labelmap ...
|
||||
reading dihedral labelmap ...
|
||||
reading improper labelmap ...
|
||||
reading atoms ...
|
||||
35200 atoms
|
||||
reading velocities ...
|
||||
35200 velocities
|
||||
scanning bonds ...
|
||||
9 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
31 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
33600 bonds
|
||||
reading angles ...
|
||||
59200 angles
|
||||
reading dihedrals ...
|
||||
80000 dihedrals
|
||||
reading impropers ...
|
||||
35200 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
41 = max # of special neighbors
|
||||
special bonds CPU = 0.007 seconds
|
||||
read_data CPU = 0.853 seconds
|
||||
Read molecule template mol1:
|
||||
1 molecules
|
||||
0 fragments
|
||||
18 atoms with max type 8
|
||||
16 bonds with max type 12
|
||||
25 angles with max type 24
|
||||
23 dihedrals with max type 33
|
||||
2 impropers with max type 9
|
||||
Read molecule template mol2:
|
||||
1 molecules
|
||||
0 fragments
|
||||
18 atoms with max type 9
|
||||
17 bonds with max type 11
|
||||
31 angles with max type 23
|
||||
39 dihedrals with max type 30
|
||||
0 impropers with max type 0
|
||||
Read molecule template mol3:
|
||||
1 molecules
|
||||
0 fragments
|
||||
15 atoms with max type 9
|
||||
14 bonds with max type 11
|
||||
25 angles with max type 23
|
||||
30 dihedrals with max type 30
|
||||
0 impropers with max type 0
|
||||
Read molecule template mol4:
|
||||
1 molecules
|
||||
0 fragments
|
||||
15 atoms with max type 11
|
||||
13 bonds with max type 13
|
||||
19 angles with max type 25
|
||||
16 dihedrals with max type 29
|
||||
2 impropers with max type 11
|
||||
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
|
||||
The log file lists these citations in BibTeX format.
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20765034
|
||||
grid = 18 18 18
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.033315619
|
||||
estimated relative force accuracy = 0.000100329
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 4508 1620
|
||||
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 15 15 15
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 81.39 | 81.41 | 81.43 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 800 3666.3948 0.80366765 0 0
|
||||
50 673.94821 -9679.5038 0.80366765 31 0
|
||||
100 694.36354 -2108.4881 0.80366765 57 22
|
||||
150 716.5075 -12356.04 0.80366765 77 50
|
||||
200 722.97306 -1308.3439 0.80366765 84 67
|
||||
Loop time of 23.0703 on 4 procs for 200 steps with 35200 atoms
|
||||
|
||||
Performance: 0.749 ns/day, 32.042 hours/ns, 8.669 timesteps/s, 305.154 katom-step/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.6778 | 6.8513 | 6.9896 | 5.2 | 29.70
|
||||
Bond | 3.8962 | 3.9719 | 4.0488 | 3.0 | 17.22
|
||||
Kspace | 1.1907 | 1.3846 | 1.6278 | 15.9 | 6.00
|
||||
Neigh | 8.7963 | 8.7965 | 8.7967 | 0.0 | 38.13
|
||||
Comm | 0.1468 | 0.15512 | 0.16131 | 1.6 | 0.67
|
||||
Output | 0.00035931 | 0.00037432 | 0.00041707 | 0.0 | 0.00
|
||||
Modify | 1.8808 | 1.8808 | 1.8809 | 0.0 | 8.15
|
||||
Other | | 0.02973 | | | 0.13
|
||||
|
||||
Nlocal: 8800 ave 8911 max 8662 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 18358.5 ave 18438 max 18183 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
Neighs: 1.73191e+06 ave 1.77313e+06 max 1.68375e+06 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 6927655
|
||||
Ave neighs/atom = 196.80838
|
||||
Ave special neighs/atom = 9.8480114
|
||||
Neighbor list builds = 128
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:24
|
||||
@ -1,189 +0,0 @@
|
||||
this is a molecule template for: initial nylon crosslink, post-reacting
|
||||
|
||||
18 atoms
|
||||
17 bonds
|
||||
31 angles
|
||||
39 dihedrals
|
||||
20 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 9
|
||||
2 1
|
||||
3 1
|
||||
4 4
|
||||
5 4
|
||||
6 3
|
||||
7 3
|
||||
8 1
|
||||
9 1
|
||||
10 5
|
||||
11 8
|
||||
12 6
|
||||
13 3
|
||||
14 3
|
||||
15 7
|
||||
16 1
|
||||
17 3
|
||||
18 3
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
16 0.000000
|
||||
17 0.000000
|
||||
18 0.000000
|
||||
|
||||
Coords
|
||||
|
||||
1 -5.522237 -0.752722 1.631158
|
||||
2 -5.170398 -0.545733 0.178130
|
||||
3 -6.469695 -0.553072 -0.648889
|
||||
4 -6.052076 -1.721152 1.744648
|
||||
5 -6.183059 0.071387 1.971497
|
||||
6 -4.489340 -1.389197 -0.173156
|
||||
7 -4.637591 0.453703 0.051252
|
||||
8 -5.618658 0.138919 4.386107
|
||||
9 -4.669492 -0.989819 3.943591
|
||||
10 -4.270194 -0.766405 2.474102
|
||||
11 -3.348470 -1.875393 2.024289
|
||||
12 -3.569794 0.564183 2.345995
|
||||
13 -5.201079 -1.993301 4.044219
|
||||
14 -3.736682 -0.984819 4.598305
|
||||
15 -4.255402 1.370923 2.679069
|
||||
16 -6.136394 -0.339866 -2.136775
|
||||
17 -6.996331 -1.555519 -0.517408
|
||||
18 -7.153308 0.284949 -0.289930
|
||||
|
||||
Bonds
|
||||
|
||||
1 9 1 2
|
||||
2 10 1 4
|
||||
3 10 1 5
|
||||
4 11 1 10
|
||||
5 1 2 3
|
||||
6 2 2 6
|
||||
7 2 2 7
|
||||
8 1 3 16
|
||||
9 2 3 17
|
||||
10 2 3 18
|
||||
11 1 8 9
|
||||
12 6 9 10
|
||||
13 2 9 13
|
||||
14 2 9 14
|
||||
15 7 10 11
|
||||
16 5 10 12
|
||||
17 8 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 14 2 1 4
|
||||
2 14 2 1 5
|
||||
3 15 2 1 10
|
||||
4 16 4 1 5
|
||||
5 17 4 1 10
|
||||
6 17 5 1 10
|
||||
7 18 1 2 3
|
||||
8 19 1 2 6
|
||||
9 19 1 2 7
|
||||
10 1 3 2 6
|
||||
11 1 3 2 7
|
||||
12 3 6 2 7
|
||||
13 2 2 3 16
|
||||
14 1 2 3 17
|
||||
15 1 2 3 18
|
||||
16 1 16 3 17
|
||||
17 1 16 3 18
|
||||
18 3 17 3 18
|
||||
19 12 8 9 10
|
||||
20 1 8 9 13
|
||||
21 1 8 9 14
|
||||
22 13 13 9 10
|
||||
23 13 14 9 10
|
||||
24 3 13 9 14
|
||||
25 10 9 10 11
|
||||
26 8 9 10 12
|
||||
27 20 1 10 9
|
||||
28 21 11 10 12
|
||||
29 22 1 10 11
|
||||
30 23 1 10 12
|
||||
31 11 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 16 4 1 2 3
|
||||
2 17 4 1 2 6
|
||||
3 17 4 1 2 7
|
||||
4 16 5 1 2 3
|
||||
5 17 5 1 2 6
|
||||
6 17 5 1 2 7
|
||||
7 18 10 1 2 3
|
||||
8 19 10 1 2 6
|
||||
9 19 10 1 2 7
|
||||
10 20 2 1 10 9
|
||||
11 21 2 1 10 11
|
||||
12 22 2 1 10 12
|
||||
13 23 4 1 10 9
|
||||
14 24 4 1 10 11
|
||||
15 25 4 1 10 12
|
||||
16 23 5 1 10 9
|
||||
17 24 5 1 10 11
|
||||
18 25 5 1 10 12
|
||||
19 26 1 2 3 16
|
||||
20 27 1 2 3 17
|
||||
21 27 1 2 3 18
|
||||
22 4 16 3 2 6
|
||||
23 2 6 2 3 17
|
||||
24 2 6 2 3 18
|
||||
25 4 16 3 2 7
|
||||
26 2 7 2 3 17
|
||||
27 2 7 2 3 18
|
||||
28 14 8 9 10 11
|
||||
29 12 8 9 10 12
|
||||
30 28 8 9 10 1
|
||||
31 15 13 9 10 11
|
||||
32 13 13 9 10 12
|
||||
33 29 13 9 10 1
|
||||
34 15 14 9 10 11
|
||||
35 13 14 9 10 12
|
||||
36 29 14 9 10 1
|
||||
37 10 9 10 12 15
|
||||
38 11 11 10 12 15
|
||||
39 30 1 10 12 15
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 2 1 4 5
|
||||
2 1 2 1 4 10
|
||||
3 1 2 1 5 10
|
||||
4 1 4 1 5 10
|
||||
5 1 1 2 3 6
|
||||
6 1 1 2 3 7
|
||||
7 1 1 2 6 7
|
||||
8 1 3 2 6 7
|
||||
9 1 2 3 16 17
|
||||
10 1 2 3 16 18
|
||||
11 1 2 3 17 18
|
||||
12 1 16 3 17 18
|
||||
13 1 8 9 13 10
|
||||
14 1 8 9 14 10
|
||||
15 1 8 9 13 14
|
||||
16 1 13 9 14 10
|
||||
17 1 9 10 11 12
|
||||
18 1 1 10 9 11
|
||||
19 1 1 10 9 12
|
||||
20 1 1 10 11 12
|
||||
@ -0,0 +1,187 @@
|
||||
this is a molecule template for: initial nylon crosslink, post-reacting
|
||||
|
||||
18 atoms
|
||||
17 bonds
|
||||
31 angles
|
||||
39 dihedrals
|
||||
0 impropers
|
||||
|
||||
Coords
|
||||
|
||||
1 -5.522237178 -0.752722499 1.631158408
|
||||
2 -5.170398325 -0.545733378 0.178129978
|
||||
3 -6.469694974 -0.553071841 -0.648889109
|
||||
4 -6.052075697 -1.721152483 1.744647858
|
||||
5 -6.183058842 0.071386755 1.971497329
|
||||
6 -4.489339595 -1.389196844 -0.173156276
|
||||
7 -4.637590712 0.453703382 0.051251954
|
||||
8 -5.618657658 0.138918810 4.386106928
|
||||
9 -4.669491736 -0.989818781 3.943591338
|
||||
10 -4.270193542 -0.766405234 2.474102239
|
||||
11 -3.348470373 -1.875393291 2.024289246
|
||||
12 -3.569793683 0.564183226 2.345995471
|
||||
13 -5.201078949 -1.993301389 4.044218837
|
||||
14 -3.736681607 -0.984819193 4.598304847
|
||||
15 -4.255401979 1.370923174 2.679069013
|
||||
16 -6.136393628 -0.339866195 -2.136774990
|
||||
17 -6.996331494 -1.555519161 -0.517408063
|
||||
18 -7.153308038 0.284949373 -0.289930394
|
||||
|
||||
Types
|
||||
|
||||
1 n
|
||||
2 c2
|
||||
3 c2
|
||||
4 hn
|
||||
5 hn
|
||||
6 hc
|
||||
7 hc
|
||||
8 c2
|
||||
9 c2
|
||||
10 c_1
|
||||
11 o_1
|
||||
12 o
|
||||
13 hc
|
||||
14 hc
|
||||
15 ho
|
||||
16 c2
|
||||
17 hc
|
||||
18 hc
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
16 0.000000
|
||||
17 0.000000
|
||||
18 0.000000
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
|
||||
Bonds
|
||||
|
||||
1 n-c2 1 2
|
||||
2 n-hn 1 4
|
||||
3 n-hn 1 5
|
||||
4 n-c_1 1 10
|
||||
5 c2-c2 2 3
|
||||
6 c2-hc 2 6
|
||||
7 c2-hc 2 7
|
||||
8 c2-c2 3 16
|
||||
9 c2-hc 3 17
|
||||
10 c2-hc 3 18
|
||||
11 c2-c2 8 9
|
||||
12 c2-c_1 9 10
|
||||
13 c2-hc 9 13
|
||||
14 c2-hc 9 14
|
||||
15 c_1-o_1 10 11
|
||||
16 c_1-o 10 12
|
||||
17 o-ho 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 c2-n-hn 2 1 4
|
||||
2 c2-n-hn 2 1 5
|
||||
3 c2-n-c_1 2 1 10
|
||||
4 hn-n-hn 4 1 5
|
||||
5 hn-n-c_1 4 1 10
|
||||
6 hn-n-c_1 5 1 10
|
||||
7 n-c2-c2 1 2 3
|
||||
8 n-c2-hc 1 2 6
|
||||
9 n-c2-hc 1 2 7
|
||||
10 c2-c2-hc 3 2 6
|
||||
11 c2-c2-hc 3 2 7
|
||||
12 hc-c2-hc 6 2 7
|
||||
13 c2-c2-c2 2 3 16
|
||||
14 c2-c2-hc 2 3 17
|
||||
15 c2-c2-hc 2 3 18
|
||||
16 c2-c2-hc 16 3 17
|
||||
17 c2-c2-hc 16 3 18
|
||||
18 hc-c2-hc 17 3 18
|
||||
19 c2-c2-c_1 8 9 10
|
||||
20 c2-c2-hc 8 9 13
|
||||
21 c2-c2-hc 8 9 14
|
||||
22 hc-c2-c_1 13 9 10
|
||||
23 hc-c2-c_1 14 9 10
|
||||
24 hc-c2-hc 13 9 14
|
||||
25 c2-c_1-o_1 9 10 11
|
||||
26 c2-c_1-o 9 10 12
|
||||
27 n-c_1-c2 1 10 9
|
||||
28 o_1-c_1-o 11 10 12
|
||||
29 n-c_1-o_1 1 10 11
|
||||
30 n-c_1-o 1 10 12
|
||||
31 c_1-o-ho 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 hn-n-c2-c2 4 1 2 3
|
||||
2 hn-n-c2-hc 4 1 2 6
|
||||
3 hn-n-c2-hc 4 1 2 7
|
||||
4 hn-n-c2-c2 5 1 2 3
|
||||
5 hn-n-c2-hc 5 1 2 6
|
||||
6 hn-n-c2-hc 5 1 2 7
|
||||
7 c_1-n-c2-c2 10 1 2 3
|
||||
8 c_1-n-c2-hc 10 1 2 6
|
||||
9 c_1-n-c2-hc 10 1 2 7
|
||||
10 c2-n-c_1-c2 2 1 10 9
|
||||
11 c2-n-c_1-o_1 2 1 10 11
|
||||
12 c2-n-c_1-o 2 1 10 12
|
||||
13 hn-n-c_1-c2 4 1 10 9
|
||||
14 hn-n-c_1-o_1 4 1 10 11
|
||||
15 hn-n-c_1-o 4 1 10 12
|
||||
16 hn-n-c_1-c2 5 1 10 9
|
||||
17 hn-n-c_1-o_1 5 1 10 11
|
||||
18 hn-n-c_1-o 5 1 10 12
|
||||
19 n-c2-c2-c2 1 2 3 16
|
||||
20 n-c2-c2-hc 1 2 3 17
|
||||
21 n-c2-c2-hc 1 2 3 18
|
||||
22 c2-c2-c2-hc 16 3 2 6
|
||||
23 hc-c2-c2-hc 6 2 3 17
|
||||
24 hc-c2-c2-hc 6 2 3 18
|
||||
25 c2-c2-c2-hc 16 3 2 7
|
||||
26 hc-c2-c2-hc 7 2 3 17
|
||||
27 hc-c2-c2-hc 7 2 3 18
|
||||
28 c2-c2-c_1-o_1 8 9 10 11
|
||||
29 c2-c2-c_1-o 8 9 10 12
|
||||
30 c2-c2-c_1-n 8 9 10 1
|
||||
31 hc-c2-c_1-o_1 13 9 10 11
|
||||
32 hc-c2-c_1-o 13 9 10 12
|
||||
33 hc-c2-c_1-n 13 9 10 1
|
||||
34 hc-c2-c_1-o_1 14 9 10 11
|
||||
35 hc-c2-c_1-o 14 9 10 12
|
||||
36 hc-c2-c_1-n 14 9 10 1
|
||||
37 c2-c_1-o-ho 9 10 12 15
|
||||
38 o_1-c_1-o-ho 11 10 12 15
|
||||
39 n-c_1-o-ho 1 10 12 15
|
||||
@ -1,160 +0,0 @@
|
||||
this is a molecule template for: initial nylon crosslink, pre-reacting
|
||||
|
||||
18 atoms
|
||||
16 bonds
|
||||
25 angles
|
||||
23 dihedrals
|
||||
14 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 2
|
||||
2 1
|
||||
3 1
|
||||
4 4
|
||||
5 4
|
||||
6 3
|
||||
7 3
|
||||
8 1
|
||||
9 1
|
||||
10 5
|
||||
11 8
|
||||
12 6
|
||||
13 3
|
||||
14 3
|
||||
15 7
|
||||
16 1
|
||||
17 3
|
||||
18 3
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
16 0.000000
|
||||
17 0.000000
|
||||
18 0.000000
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.922858 -0.946982 1.146055
|
||||
2 -5.047195 -0.935267 -0.358173
|
||||
3 -6.526281 -0.755366 -0.743523
|
||||
4 -5.282604 0.020447 1.552710
|
||||
5 -3.860697 -1.095850 1.428305
|
||||
6 -4.662382 -1.920900 -0.781524
|
||||
7 -4.433977 -0.072765 -0.784071
|
||||
8 -5.506279 0.202610 4.825816
|
||||
9 -4.449177 -0.844592 4.423366
|
||||
10 -4.103916 -0.749629 2.925195
|
||||
11 -3.376249 -1.886171 2.245643
|
||||
12 -4.493235 0.477214 2.137199
|
||||
13 -4.849053 -1.888877 4.663994
|
||||
14 -3.491823 -0.662913 5.018510
|
||||
15 -5.020777 1.189745 2.805427
|
||||
16 -3.964987 2.900602 -1.551341
|
||||
17 -4.460694 2.836102 0.668882
|
||||
18 -4.828494 3.219656 -0.122111
|
||||
|
||||
Bonds
|
||||
|
||||
1 12 1 2
|
||||
2 4 1 4
|
||||
3 4 1 5
|
||||
4 1 2 3
|
||||
5 2 2 6
|
||||
6 2 2 7
|
||||
7 1 3 16
|
||||
8 2 3 17
|
||||
9 2 3 18
|
||||
10 1 8 9
|
||||
11 6 9 10
|
||||
12 2 9 13
|
||||
13 2 9 14
|
||||
14 7 10 11
|
||||
15 5 10 12
|
||||
16 8 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 6 2 1 4
|
||||
2 6 2 1 5
|
||||
3 7 4 1 5
|
||||
4 24 1 2 3
|
||||
5 5 1 2 6
|
||||
6 5 1 2 7
|
||||
7 1 3 2 6
|
||||
8 1 3 2 7
|
||||
9 3 6 2 7
|
||||
10 2 2 3 16
|
||||
11 1 2 3 17
|
||||
12 1 2 3 18
|
||||
13 1 16 3 17
|
||||
14 1 16 3 18
|
||||
15 3 17 3 18
|
||||
16 12 8 9 10
|
||||
17 1 8 9 13
|
||||
18 1 8 9 14
|
||||
19 13 13 9 10
|
||||
20 13 14 9 10
|
||||
21 3 13 9 14
|
||||
22 10 9 10 11
|
||||
23 8 9 10 12
|
||||
24 21 11 10 12
|
||||
25 11 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 31 4 1 2 3
|
||||
2 32 4 1 2 6
|
||||
3 32 4 1 2 7
|
||||
4 31 5 1 2 3
|
||||
5 32 5 1 2 6
|
||||
6 32 5 1 2 7
|
||||
7 33 1 2 3 16
|
||||
8 1 1 2 3 17
|
||||
9 1 1 2 3 18
|
||||
10 4 16 3 2 6
|
||||
11 2 6 2 3 17
|
||||
12 2 6 2 3 18
|
||||
13 4 16 3 2 7
|
||||
14 2 7 2 3 17
|
||||
15 2 7 2 3 18
|
||||
16 14 8 9 10 11
|
||||
17 12 8 9 10 12
|
||||
18 15 13 9 10 11
|
||||
19 13 13 9 10 12
|
||||
20 15 14 9 10 11
|
||||
21 13 14 9 10 12
|
||||
22 10 9 10 12 15
|
||||
23 11 11 10 12 15
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 2 1 4 5
|
||||
2 9 9 10 11 12
|
||||
3 1 1 2 3 6
|
||||
4 1 1 2 3 7
|
||||
5 1 1 2 6 7
|
||||
6 1 3 2 6 7
|
||||
7 1 2 3 16 17
|
||||
8 1 2 3 16 18
|
||||
9 1 2 3 17 18
|
||||
10 1 16 3 17 18
|
||||
11 1 8 9 13 10
|
||||
12 1 8 9 14 10
|
||||
13 1 8 9 13 14
|
||||
14 1 13 9 14 10
|
||||
@ -0,0 +1,169 @@
|
||||
this is a molecule template for: initial nylon crosslink, pre-reacting
|
||||
|
||||
18 atoms
|
||||
16 bonds
|
||||
25 angles
|
||||
23 dihedrals
|
||||
2 impropers
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.922858499 -0.946981747 1.146055346
|
||||
2 -5.047194816 -0.935266843 -0.358172771
|
||||
3 -6.526281447 -0.755365854 -0.743523227
|
||||
4 -5.282604074 0.020446894 1.552710361
|
||||
5 -3.860696509 -1.095850190 1.428304925
|
||||
6 -4.662381862 -1.920899862 -0.781524026
|
||||
7 -4.433976540 -0.072765142 -0.784070641
|
||||
8 -5.506279186 0.202610302 4.825815562
|
||||
9 -4.449176624 -0.844592213 4.423366146
|
||||
10 -4.103915981 -0.749628655 2.925195217
|
||||
11 -3.376248536 -1.886171498 2.245643443
|
||||
12 -4.493235430 0.477213651 2.137199034
|
||||
13 -4.849052953 -1.888876753 4.663993750
|
||||
14 -3.491822950 -0.662913310 5.018510248
|
||||
15 -5.020776528 1.189745133 2.805427194
|
||||
16 -3.964987378 2.900602044 -1.551341170
|
||||
17 -4.460693773 2.836101897 0.668881952
|
||||
18 -4.828494000 3.219655862 -0.122111278
|
||||
|
||||
Types
|
||||
|
||||
1 na
|
||||
2 c2
|
||||
3 c2
|
||||
4 hn
|
||||
5 hn
|
||||
6 hc
|
||||
7 hc
|
||||
8 c2
|
||||
9 c2
|
||||
10 c_1
|
||||
11 o_1
|
||||
12 o
|
||||
13 hc
|
||||
14 hc
|
||||
15 ho
|
||||
16 c2
|
||||
17 hc
|
||||
18 hc
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
16 0.000000
|
||||
17 0.000000
|
||||
18 0.000000
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
|
||||
Bonds
|
||||
|
||||
1 na-c2 1 2
|
||||
2 na-hn 1 4
|
||||
3 na-hn 1 5
|
||||
4 c2-c2 2 3
|
||||
5 c2-hc 2 6
|
||||
6 c2-hc 2 7
|
||||
7 c2-c2 3 16
|
||||
8 c2-hc 3 17
|
||||
9 c2-hc 3 18
|
||||
10 c2-c2 8 9
|
||||
11 c2-c_1 9 10
|
||||
12 c2-hc 9 13
|
||||
13 c2-hc 9 14
|
||||
14 c_1-o_1 10 11
|
||||
15 c_1-o 10 12
|
||||
16 o-ho 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 c2-na-hn 2 1 4
|
||||
2 c2-na-hn 2 1 5
|
||||
3 hn-na-hn 4 1 5
|
||||
4 na-c2-c2 1 2 3
|
||||
5 na-c2-hc 1 2 6
|
||||
6 na-c2-hc 1 2 7
|
||||
7 c2-c2-hc 3 2 6
|
||||
8 c2-c2-hc 3 2 7
|
||||
9 hc-c2-hc 6 2 7
|
||||
10 c2-c2-c2 2 3 16
|
||||
11 c2-c2-hc 2 3 17
|
||||
12 c2-c2-hc 2 3 18
|
||||
13 c2-c2-hc 16 3 17
|
||||
14 c2-c2-hc 16 3 18
|
||||
15 hc-c2-hc 17 3 18
|
||||
16 c2-c2-c_1 8 9 10
|
||||
17 c2-c2-hc 8 9 13
|
||||
18 c2-c2-hc 8 9 14
|
||||
19 hc-c2-c_1 13 9 10
|
||||
20 hc-c2-c_1 14 9 10
|
||||
21 hc-c2-hc 13 9 14
|
||||
22 c2-c_1-o_1 9 10 11
|
||||
23 c2-c_1-o 9 10 12
|
||||
24 o_1-c_1-o 11 10 12
|
||||
25 c_1-o-ho 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 hn-na-c2-c2 4 1 2 3
|
||||
2 hn-na-c2-hc 4 1 2 6
|
||||
3 hn-na-c2-hc 4 1 2 7
|
||||
4 hn-na-c2-c2 5 1 2 3
|
||||
5 hn-na-c2-hc 5 1 2 6
|
||||
6 hn-na-c2-hc 5 1 2 7
|
||||
7 na-c2-c2-c2 1 2 3 16
|
||||
8 na-c2-c2-hc 1 2 3 17
|
||||
9 na-c2-c2-hc 1 2 3 18
|
||||
10 c2-c2-c2-hc 16 3 2 6
|
||||
11 hc-c2-c2-hc 6 2 3 17
|
||||
12 hc-c2-c2-hc 6 2 3 18
|
||||
13 c2-c2-c2-hc 16 3 2 7
|
||||
14 hc-c2-c2-hc 7 2 3 17
|
||||
15 hc-c2-c2-hc 7 2 3 18
|
||||
16 c2-c2-c_1-o_1 8 9 10 11
|
||||
17 c2-c2-c_1-o 8 9 10 12
|
||||
18 hc-c2-c_1-o_1 13 9 10 11
|
||||
19 hc-c2-c_1-o 13 9 10 12
|
||||
20 hc-c2-c_1-o_1 14 9 10 11
|
||||
21 hc-c2-c_1-o 14 9 10 12
|
||||
22 c2-c_1-o-ho 9 10 12 15
|
||||
23 o_1-c_1-o-ho 11 10 12 15
|
||||
|
||||
Impropers
|
||||
|
||||
1 c2-na-hn-hn 2 1 4 5
|
||||
2 c2-c_1-o_1-o 9 10 11 12
|
||||
@ -1,131 +0,0 @@
|
||||
this is a molecule template for: water condensation, post-reacting
|
||||
|
||||
15 atoms
|
||||
13 bonds
|
||||
19 angles
|
||||
16 dihedrals
|
||||
10 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 9
|
||||
2 1
|
||||
3 1
|
||||
4 10
|
||||
5 4
|
||||
6 3
|
||||
7 3
|
||||
8 1
|
||||
9 1
|
||||
10 5
|
||||
11 8
|
||||
12 11
|
||||
13 3
|
||||
14 3
|
||||
15 10
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.410000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 -0.820000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.410000
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.856280 -1.050468 1.432625
|
||||
2 -5.047195 -0.935267 -0.358173
|
||||
3 -6.526281 -0.755366 -0.743523
|
||||
4 -5.282604 0.020447 1.552710
|
||||
5 -3.860697 -1.095850 1.428305
|
||||
6 -4.662382 -1.920900 -0.781524
|
||||
7 -4.433977 -0.072765 -0.784071
|
||||
8 -5.506279 0.202610 4.825816
|
||||
9 -4.449177 -0.844592 4.423366
|
||||
10 -4.103916 -0.749629 2.925195
|
||||
11 -3.376249 -1.886171 2.245643
|
||||
12 -4.493235 0.477214 2.137199
|
||||
13 -4.849053 -1.888877 4.663994
|
||||
14 -3.491823 -0.662913 5.018510
|
||||
15 -5.020777 1.189745 2.805427
|
||||
|
||||
Bonds
|
||||
|
||||
1 9 1 2
|
||||
2 10 1 5
|
||||
3 11 1 10
|
||||
4 1 2 3
|
||||
5 2 2 6
|
||||
6 2 2 7
|
||||
7 13 4 12
|
||||
8 1 8 9
|
||||
9 6 9 10
|
||||
10 2 9 13
|
||||
11 2 9 14
|
||||
12 7 10 11
|
||||
13 13 15 12
|
||||
|
||||
Angles
|
||||
|
||||
1 14 2 1 5
|
||||
2 15 2 1 10
|
||||
3 17 5 1 10
|
||||
4 18 1 2 3
|
||||
5 19 1 2 6
|
||||
6 19 1 2 7
|
||||
7 1 3 2 6
|
||||
8 1 3 2 7
|
||||
9 3 6 2 7
|
||||
10 12 8 9 10
|
||||
11 1 8 9 13
|
||||
12 1 8 9 14
|
||||
13 13 13 9 10
|
||||
14 13 14 9 10
|
||||
15 3 13 9 14
|
||||
16 10 9 10 11
|
||||
17 20 1 10 9
|
||||
18 22 1 10 11
|
||||
19 25 15 12 4
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 16 5 1 2 3
|
||||
2 17 5 1 2 6
|
||||
3 17 5 1 2 7
|
||||
4 18 10 1 2 3
|
||||
5 19 10 1 2 6
|
||||
6 19 10 1 2 7
|
||||
7 20 2 1 10 9
|
||||
8 21 2 1 10 11
|
||||
9 23 5 1 10 9
|
||||
10 24 5 1 10 11
|
||||
11 14 8 9 10 11
|
||||
12 28 8 9 10 1
|
||||
13 15 13 9 10 11
|
||||
14 29 13 9 10 1
|
||||
15 15 14 9 10 11
|
||||
16 29 14 9 10 1
|
||||
|
||||
Impropers
|
||||
|
||||
1 10 2 1 5 10
|
||||
2 11 1 10 9 11
|
||||
3 1 1 2 3 6
|
||||
4 1 1 2 3 7
|
||||
5 1 1 2 6 7
|
||||
6 1 3 2 6 7
|
||||
7 1 8 9 13 10
|
||||
8 1 8 9 14 10
|
||||
9 1 8 9 13 14
|
||||
10 1 13 9 14 10
|
||||
@ -0,0 +1,141 @@
|
||||
this is a molecule template for: water condensation, post-reacting
|
||||
|
||||
15 atoms
|
||||
13 bonds
|
||||
19 angles
|
||||
16 dihedrals
|
||||
2 impropers
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.856280281 -1.050467974 1.432625159
|
||||
2 -5.047194816 -0.935266843 -0.358172771
|
||||
3 -6.526281447 -0.755365854 -0.743523227
|
||||
4 -5.282604074 0.020446894 1.552710361
|
||||
5 -3.860696509 -1.095850190 1.428304925
|
||||
6 -4.662381862 -1.920899862 -0.781524026
|
||||
7 -4.433976540 -0.072765142 -0.784070641
|
||||
8 -5.506279186 0.202610302 4.825815562
|
||||
9 -4.449176624 -0.844592213 4.423366146
|
||||
10 -4.103915981 -0.749628655 2.925195217
|
||||
11 -3.376248536 -1.886171498 2.245643443
|
||||
12 -4.493235430 0.477213651 2.137199034
|
||||
13 -4.849052953 -1.888876753 4.663993750
|
||||
14 -3.491822950 -0.662913310 5.018510248
|
||||
15 -5.020776528 1.189745133 2.805427194
|
||||
|
||||
Types
|
||||
|
||||
1 n
|
||||
2 c2
|
||||
3 c2
|
||||
4 hw
|
||||
5 hn
|
||||
6 hc
|
||||
7 hc
|
||||
8 c2
|
||||
9 c2
|
||||
10 c_1
|
||||
11 o_1
|
||||
12 o*
|
||||
13 hc
|
||||
14 hc
|
||||
15 hw
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.410000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 -0.820000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.410000
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
|
||||
Bonds
|
||||
|
||||
1 n-c2 1 2
|
||||
2 n-hn 1 5
|
||||
3 n-c_1 1 10
|
||||
4 c2-c2 2 3
|
||||
5 c2-hc 2 6
|
||||
6 c2-hc 2 7
|
||||
7 hw-o* 4 12
|
||||
8 c2-c2 8 9
|
||||
9 c2-c_1 9 10
|
||||
10 c2-hc 9 13
|
||||
11 c2-hc 9 14
|
||||
12 c_1-o_1 10 11
|
||||
13 hw-o* 15 12
|
||||
|
||||
Angles
|
||||
|
||||
1 c2-n-hn 2 1 5
|
||||
2 c2-n-c_1 2 1 10
|
||||
3 hn-n-c_1 5 1 10
|
||||
4 n-c2-c2 1 2 3
|
||||
5 n-c2-hc 1 2 6
|
||||
6 n-c2-hc 1 2 7
|
||||
7 c2-c2-hc 3 2 6
|
||||
8 c2-c2-hc 3 2 7
|
||||
9 hc-c2-hc 6 2 7
|
||||
10 c2-c2-c_1 8 9 10
|
||||
11 c2-c2-hc 8 9 13
|
||||
12 c2-c2-hc 8 9 14
|
||||
13 hc-c2-c_1 13 9 10
|
||||
14 hc-c2-c_1 14 9 10
|
||||
15 hc-c2-hc 13 9 14
|
||||
16 c2-c_1-o_1 9 10 11
|
||||
17 n-c_1-c2 1 10 9
|
||||
18 n-c_1-o_1 1 10 11
|
||||
19 hw-o*-hw 15 12 4
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 hn-n-c2-c2 5 1 2 3
|
||||
2 hn-n-c2-hc 5 1 2 6
|
||||
3 hn-n-c2-hc 5 1 2 7
|
||||
4 c_1-n-c2-c2 10 1 2 3
|
||||
5 c_1-n-c2-hc 10 1 2 6
|
||||
6 c_1-n-c2-hc 10 1 2 7
|
||||
7 c2-n-c_1-c2 2 1 10 9
|
||||
8 c2-n-c_1-o_1 2 1 10 11
|
||||
9 hn-n-c_1-c2 5 1 10 9
|
||||
10 hn-n-c_1-o_1 5 1 10 11
|
||||
11 c2-c2-c_1-o_1 8 9 10 11
|
||||
12 c2-c2-c_1-n 8 9 10 1
|
||||
13 hc-c2-c_1-o_1 13 9 10 11
|
||||
14 hc-c2-c_1-n 13 9 10 1
|
||||
15 hc-c2-c_1-o_1 14 9 10 11
|
||||
16 hc-c2-c_1-n 14 9 10 1
|
||||
|
||||
Impropers
|
||||
|
||||
1 c2-n-hn-c_1 2 1 5 10
|
||||
2 n-c_1-c2-o_1 1 10 9 11
|
||||
@ -1,158 +0,0 @@
|
||||
this is a molecule template for: water condensation, pre-reacting
|
||||
|
||||
15 atoms
|
||||
14 bonds
|
||||
25 angles
|
||||
30 dihedrals
|
||||
16 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 9
|
||||
2 1
|
||||
3 1
|
||||
4 4
|
||||
5 4
|
||||
6 3
|
||||
7 3
|
||||
8 1
|
||||
9 1
|
||||
10 5
|
||||
11 8
|
||||
12 6
|
||||
13 3
|
||||
14 3
|
||||
15 7
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.922858 -0.946982 1.146055
|
||||
2 -5.047195 -0.935267 -0.358173
|
||||
3 -6.526281 -0.755366 -0.743523
|
||||
4 -5.282604 0.020447 1.552710
|
||||
5 -3.860697 -1.095850 1.428305
|
||||
6 -4.662382 -1.920900 -0.781524
|
||||
7 -4.433977 -0.072765 -0.784071
|
||||
8 -5.506279 0.202610 4.825816
|
||||
9 -4.449177 -0.844592 4.423366
|
||||
10 -4.103916 -0.749629 2.925195
|
||||
11 -3.376249 -1.886171 2.245643
|
||||
12 -4.493235 0.477214 2.137199
|
||||
13 -4.849053 -1.888877 4.663994
|
||||
14 -3.491823 -0.662913 5.018510
|
||||
15 -5.020777 1.189745 2.805427
|
||||
|
||||
Bonds
|
||||
|
||||
1 9 1 2
|
||||
2 10 1 4
|
||||
3 10 1 5
|
||||
4 11 1 10
|
||||
5 1 2 3
|
||||
6 2 2 6
|
||||
7 2 2 7
|
||||
8 1 8 9
|
||||
9 6 9 10
|
||||
10 2 9 13
|
||||
11 2 9 14
|
||||
12 7 10 11
|
||||
13 5 10 12
|
||||
14 8 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 14 2 1 4
|
||||
2 14 2 1 5
|
||||
3 15 2 1 10
|
||||
4 16 4 1 5
|
||||
5 17 4 1 10
|
||||
6 17 5 1 10
|
||||
7 18 1 2 3
|
||||
8 19 1 2 6
|
||||
9 19 1 2 7
|
||||
10 1 3 2 6
|
||||
11 1 3 2 7
|
||||
12 3 6 2 7
|
||||
13 12 8 9 10
|
||||
14 1 8 9 13
|
||||
15 1 8 9 14
|
||||
16 13 13 9 10
|
||||
17 13 14 9 10
|
||||
18 3 13 9 14
|
||||
19 10 9 10 11
|
||||
20 8 9 10 12
|
||||
21 20 1 10 9
|
||||
22 21 11 10 12
|
||||
23 22 1 10 11
|
||||
24 23 1 10 12
|
||||
25 11 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 16 4 1 2 3
|
||||
2 17 4 1 2 6
|
||||
3 17 4 1 2 7
|
||||
4 16 5 1 2 3
|
||||
5 17 5 1 2 6
|
||||
6 17 5 1 2 7
|
||||
7 18 10 1 2 3
|
||||
8 19 10 1 2 6
|
||||
9 19 10 1 2 7
|
||||
10 20 2 1 10 9
|
||||
11 21 2 1 10 11
|
||||
12 22 2 1 10 12
|
||||
13 23 4 1 10 9
|
||||
14 24 4 1 10 11
|
||||
15 25 4 1 10 12
|
||||
16 23 5 1 10 9
|
||||
17 24 5 1 10 11
|
||||
18 25 5 1 10 12
|
||||
19 14 8 9 10 11
|
||||
20 12 8 9 10 12
|
||||
21 28 8 9 10 1
|
||||
22 15 13 9 10 11
|
||||
23 13 13 9 10 12
|
||||
24 29 13 9 10 1
|
||||
25 15 14 9 10 11
|
||||
26 13 14 9 10 12
|
||||
27 29 14 9 10 1
|
||||
28 10 9 10 12 15
|
||||
29 11 11 10 12 15
|
||||
30 30 1 10 12 15
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 2 1 4 5
|
||||
2 1 2 1 4 10
|
||||
3 1 2 1 5 10
|
||||
4 1 4 1 5 10
|
||||
5 1 1 2 3 6
|
||||
6 1 1 2 3 7
|
||||
7 1 1 2 6 7
|
||||
8 1 3 2 6 7
|
||||
9 1 8 9 13 10
|
||||
10 1 8 9 14 10
|
||||
11 1 8 9 13 14
|
||||
12 1 13 9 14 10
|
||||
13 1 9 10 11 12
|
||||
14 1 1 10 9 11
|
||||
15 1 1 10 9 12
|
||||
16 1 1 10 11 12
|
||||
@ -0,0 +1,157 @@
|
||||
this is a molecule template for: water condensation, pre-reacting
|
||||
|
||||
15 atoms
|
||||
14 bonds
|
||||
25 angles
|
||||
30 dihedrals
|
||||
0 impropers
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.922858499 -0.946981747 1.146055346
|
||||
2 -5.047194816 -0.935266843 -0.358172771
|
||||
3 -6.526281447 -0.755365854 -0.743523227
|
||||
4 -5.282604074 0.020446894 1.552710361
|
||||
5 -3.860696509 -1.095850190 1.428304925
|
||||
6 -4.662381862 -1.920899862 -0.781524026
|
||||
7 -4.433976540 -0.072765142 -0.784070641
|
||||
8 -5.506279186 0.202610302 4.825815562
|
||||
9 -4.449176624 -0.844592213 4.423366146
|
||||
10 -4.103915981 -0.749628655 2.925195217
|
||||
11 -3.376248536 -1.886171498 2.245643443
|
||||
12 -4.493235430 0.477213651 2.137199034
|
||||
13 -4.849052953 -1.888876753 4.663993750
|
||||
14 -3.491822950 -0.662913310 5.018510248
|
||||
15 -5.020776528 1.189745133 2.805427194
|
||||
|
||||
Types
|
||||
|
||||
1 n
|
||||
2 c2
|
||||
3 c2
|
||||
4 hn
|
||||
5 hn
|
||||
6 hc
|
||||
7 hc
|
||||
8 c2
|
||||
9 c2
|
||||
10 c_1
|
||||
11 o_1
|
||||
12 o
|
||||
13 hc
|
||||
14 hc
|
||||
15 ho
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
|
||||
Bonds
|
||||
|
||||
1 n-c2 1 2
|
||||
2 n-hn 1 4
|
||||
3 n-hn 1 5
|
||||
4 n-c_1 1 10
|
||||
5 c2-c2 2 3
|
||||
6 c2-hc 2 6
|
||||
7 c2-hc 2 7
|
||||
8 c2-c2 8 9
|
||||
9 c2-c_1 9 10
|
||||
10 c2-hc 9 13
|
||||
11 c2-hc 9 14
|
||||
12 c_1-o_1 10 11
|
||||
13 c_1-o 10 12
|
||||
14 o-ho 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 c2-n-hn 2 1 4
|
||||
2 c2-n-hn 2 1 5
|
||||
3 c2-n-c_1 2 1 10
|
||||
4 hn-n-hn 4 1 5
|
||||
5 hn-n-c_1 4 1 10
|
||||
6 hn-n-c_1 5 1 10
|
||||
7 n-c2-c2 1 2 3
|
||||
8 n-c2-hc 1 2 6
|
||||
9 n-c2-hc 1 2 7
|
||||
10 c2-c2-hc 3 2 6
|
||||
11 c2-c2-hc 3 2 7
|
||||
12 hc-c2-hc 6 2 7
|
||||
13 c2-c2-c_1 8 9 10
|
||||
14 c2-c2-hc 8 9 13
|
||||
15 c2-c2-hc 8 9 14
|
||||
16 hc-c2-c_1 13 9 10
|
||||
17 hc-c2-c_1 14 9 10
|
||||
18 hc-c2-hc 13 9 14
|
||||
19 c2-c_1-o_1 9 10 11
|
||||
20 c2-c_1-o 9 10 12
|
||||
21 n-c_1-c2 1 10 9
|
||||
22 o_1-c_1-o 11 10 12
|
||||
23 n-c_1-o_1 1 10 11
|
||||
24 n-c_1-o 1 10 12
|
||||
25 c_1-o-ho 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 hn-n-c2-c2 4 1 2 3
|
||||
2 hn-n-c2-hc 4 1 2 6
|
||||
3 hn-n-c2-hc 4 1 2 7
|
||||
4 hn-n-c2-c2 5 1 2 3
|
||||
5 hn-n-c2-hc 5 1 2 6
|
||||
6 hn-n-c2-hc 5 1 2 7
|
||||
7 c_1-n-c2-c2 10 1 2 3
|
||||
8 c_1-n-c2-hc 10 1 2 6
|
||||
9 c_1-n-c2-hc 10 1 2 7
|
||||
10 c2-n-c_1-c2 2 1 10 9
|
||||
11 c2-n-c_1-o_1 2 1 10 11
|
||||
12 c2-n-c_1-o 2 1 10 12
|
||||
13 hn-n-c_1-c2 4 1 10 9
|
||||
14 hn-n-c_1-o_1 4 1 10 11
|
||||
15 hn-n-c_1-o 4 1 10 12
|
||||
16 hn-n-c_1-c2 5 1 10 9
|
||||
17 hn-n-c_1-o_1 5 1 10 11
|
||||
18 hn-n-c_1-o 5 1 10 12
|
||||
19 c2-c2-c_1-o_1 8 9 10 11
|
||||
20 c2-c2-c_1-o 8 9 10 12
|
||||
21 c2-c2-c_1-n 8 9 10 1
|
||||
22 hc-c2-c_1-o_1 13 9 10 11
|
||||
23 hc-c2-c_1-o 13 9 10 12
|
||||
24 hc-c2-c_1-n 13 9 10 1
|
||||
25 hc-c2-c_1-o_1 14 9 10 11
|
||||
26 hc-c2-c_1-o 14 9 10 12
|
||||
27 hc-c2-c_1-n 14 9 10 1
|
||||
28 c2-c_1-o-ho 9 10 12 15
|
||||
29 o_1-c_1-o-ho 11 10 12 15
|
||||
30 n-c_1-o-ho 1 10 12 15
|
||||
Reference in New Issue
Block a user