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rename examples to match usual naming conventions and add reference output.

This commit is contained in:
Axel Kohlmeyer 2018-02-01 18:56:10 +01:00
parent b70149e86a
commit 3e0cb9b463
6 changed files with 682 additions and 0 deletions
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examples/USER/mofff/hkust1.in → examples/USER/mofff/in.hkust1
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examples/USER/mofff/hkust1_long.in → examples/USER/mofff/in.hkust1_long
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examples/USER/mofff/log.17Jan18.hkust1.g++.1 Normal file
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LAMMPS (17 Jan 2018)
clear
units real
boundary p p p
atom_style full
read_data hkust1.data
triclinic box = (0 0 0) to (26.4408 26.4408 26.4408) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
624 atoms
scanning bonds ...
5 = max bonds/atom
scanning angles ...
10 = max angles/atom
scanning dihedrals ...
32 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
792 bonds
reading angles ...
1536 angles
reading dihedrals ...
2688 dihedrals
reading impropers ...
288 impropers
5 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
20 = max # of 1-4 neighbors
17 = max # of special neighbors
neighbor 2.0 bin
# ------------------------ MOF-FF FORCE FIELD ------------------------------
pair_style buck6d/coul/gauss/dsf 0.9000 12.0000
pair_coeff 1 1 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW
pair_coeff 1 2 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene
pair_coeff 1 3 6157.8178 3.4682081 129.19572 0.78772886 0.73006542 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 1 4 23689.598 2.8436019 1636.052 12.696549 0.42066711 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 1 5 10576.399 3.1746032 377.27092 2.7176691 0.61999948 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 1 6 10304 3.0769231 443.36171 4.2093581 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 2 2 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene
pair_coeff 2 3 6157.8178 3.4682081 129.19572 0.78772886 0.73006542 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 2 4 23689.598 2.8436019 1636.052 12.696549 0.42066711 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 2 5 10576.399 3.1746032 377.27092 2.7176691 0.61999948 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 2 6 10304 3.0769231 443.36171 4.2093581 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 3 3 3680 4 32.805 0.10690769 0.9771554 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 3 4 14157.243 3.1914894 489.18197 2.5231391 0.45538909 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 3 5 6320.6076 3.6144578 103.50278 0.44181916 0.75109952 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 3 6 6157.8178 3.4883721 124.7792 0.72632262 0.73006542 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 4 4 54464 2.6548673 5679.4311 33.208515 0.34105936 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 4 5 24315.863 2.9411765 1371.5617 7.9168726 0.42457748 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 4 6 23689.598 2.8571429 1590.0769 11.87959 0.42066711 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 5 5 10856 3.2967033 308.7755 1.6022517 0.63272774 # buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 5 6 10576.399 3.1914894 365.45138 2.5231391 0.61999948 # buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 6 6 10304 3.0927835 429.89352 3.9170177 0.60800971 # buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
bond_style hybrid class2 morse
bond_coeff 5 morse 50.000000 1.451345 1.914000 # morse->(cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
bond_coeff 4 class2 2.536000 75.465060 -192.435903 286.248406 # mm3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2)|CuPW
bond_coeff 3 class2 1.094000 390.634200 -996.117210 1481.724350 # mm3->(c3_c2h1@ph,h1_c1@ph)|benzene
bond_coeff 6 class2 1.278000 585.591600 -1493.258580 2221.222138 # mm3->(c3_c1o2@co2,o2_c1cu1@co2)|CuPW
bond_coeff 1 class2 1.394000 509.335200 -1298.804760 1931.972080 # mm3->(c3_c2h1@ph,c3_c2h1@ph)|benzene
bond_coeff 2 class2 1.485000 360.635220 -919.619811 1367.934469 # mm3->(c3_c1o2@co2,c3_c3@ph)|CuPW
angle_style hybrid class2/p6 cosine/buck6d
angle_coeff 2 class2/p6 117.711000 57.408120 -46.049402 10.553745 -7.558563 13.610890 # mm3->(c3_c1o2@co2,c3_c3@ph,c3_c2h1@ph)|CuPW
angle_coeff 2 class2/p6 bb 0.0 1.0 1.0
angle_coeff 2 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 6 class2/p6 126.814000 13.740540 -11.021849 2.526022 -1.809130 3.257744 # mm3->(c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
angle_coeff 6 class2/p6 bb 0.0 1.0 1.0
angle_coeff 6 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 7 class2/p6 123.490000 111.075360 -89.098091 20.419778 -14.624589 26.334856 # mm3->(o2_c1cu1@co2,c3_c1o2@co2,o2_c1cu1@co2)|CuPW
angle_coeff 7 class2/p6 bb 14.244120 1.278000 1.278000
angle_coeff 7 class2/p6 ba 3.309240 3.309240 1.278000 1.278000
angle_coeff 1 class2/p6 127.050000 53.307540 -42.760159 9.799907 -7.018666 12.638684 # mm3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph)|benzene
angle_coeff 1 class2/p6 bb 71.796120 1.394000 1.394000
angle_coeff 1 class2/p6 ba 6.762360 6.762360 1.394000 1.394000
angle_coeff 4 class2/p6 84.336000 29.351520 -23.544055 5.395900 -3.864529 6.958951 # mm3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
angle_coeff 4 class2/p6 bb 0.0 1.0 1.0
angle_coeff 4 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 3 class2/p6 120.350000 36.185820 -29.026127 6.652298 -4.764358 8.579296 # mm3->(c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
angle_coeff 3 class2/p6 bb 93.378120 1.394000 1.094000
angle_coeff 3 class2/p6 ba -25.179000 53.523360 1.394000 1.094000
angle_coeff 8 class2/p6 115.098000 79.493700 -63.765149 14.613896 -10.466432 18.847160 # mm3->(c3_c3@ph,c3_c1o2@co2,o2_c1cu1@co2)|CuPW
angle_coeff 8 class2/p6 bb 0.0 1.0 1.0
angle_coeff 8 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 5 cosine/buck6d 1.978350 4 180.000000 # fourier->(o2_c1cu1@co2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
dihedral_style opls
dihedral_coeff 3 0.000000 0.000000 0.000000 0.000000 # cos3->(c3_c3@ph,c3_c2h1@ph,c3_c3@ph,c3_c1o2@co2)|CuPW
dihedral_coeff 9 0.000000 4.528000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
dihedral_coeff 8 0.000000 0.000000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,cu5_cu1o4@cu2,o2_c1cu1@co2,c3_c1o2@co2)|CuPW
dihedral_coeff 5 0.000000 1.741000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,c3_c1o2@co2,c3_c3@ph,c3_c2h1@ph)|CuPW
dihedral_coeff 2 0.000000 6.316000 0.000000 0.000000 # cos3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
dihedral_coeff 1 0.000000 4.379000 0.000000 0.000000 # cos3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph)|benzene
dihedral_coeff 6 0.000000 0.000000 0.000000 0.609000 # cos4->(o2_c1cu1@co2,cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
dihedral_coeff 4 0.000000 0.000000 0.000000 0.000000 # cos3->(h1_c1@ph,c3_c2h1@ph,c3_c3@ph,c3_c1o2@co2)|CuPW
dihedral_coeff 10 0.000000 0.000000 0.000000 0.000000 # cos3->(c3_c3@ph,c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
dihedral_coeff 7 0.000000 0.000000 0.000000 0.000000 # cos3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2,c3_c1o2@co2)|CuPW
improper_style inversion/harmonic
improper_coeff 1 18.776340 0.000000 # harm->(c3_c3@ph,c3_c2h1@ph,c3_c2h1@ph,c3_c1o2@co2)|CuPW
improper_coeff 3 41.005800 0.000000 # harm->(c3_c1o2@co2,c3_c3@ph,o2_c1cu1@co2,o2_c1cu1@co2)|CuPW
improper_coeff 2 4.100580 0.000000 # harm->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0
5 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of special neighbors
# ------------------------ MOF-FF FORCE FIELD END --------------------------
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair buck6d/coul/gauss/dsf, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 21.23 | 21.23 | 21.23 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -11833.81 343.7619 -11490.048 -5.8508834
Loop time of 9.53674e-07 on 1 procs for 0 steps with 624 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 624 ave 624 max 624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4464 ave 4464 max 4464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 115368 ave 115368 max 115368 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 115368
Ave neighs/atom = 184.885
Ave special neighs/atom = 7.46154
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (17 Jan 2018)
clear
units real
boundary p p p
atom_style full
read_data hkust1.data
triclinic box = (0 0 0) to (26.4408 26.4408 26.4408) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
624 atoms
scanning bonds ...
5 = max bonds/atom
scanning angles ...
10 = max angles/atom
scanning dihedrals ...
32 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
792 bonds
reading angles ...
1536 angles
reading dihedrals ...
2688 dihedrals
reading impropers ...
288 impropers
5 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
20 = max # of 1-4 neighbors
17 = max # of special neighbors
neighbor 2.0 bin
# ------------------------ MOF-FF FORCE FIELD ------------------------------
pair_style buck6d/coul/gauss/dsf 0.9000 12.0000
pair_coeff 1 1 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW
pair_coeff 1 2 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene
pair_coeff 1 3 6157.8178 3.4682081 129.19572 0.78772886 0.73006542 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 1 4 23689.598 2.8436019 1636.052 12.696549 0.42066711 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 1 5 10576.399 3.1746032 377.27092 2.7176691 0.61999948 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 1 6 10304 3.0769231 443.36171 4.2093581 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 2 2 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene
pair_coeff 2 3 6157.8178 3.4682081 129.19572 0.78772886 0.73006542 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 2 4 23689.598 2.8436019 1636.052 12.696549 0.42066711 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 2 5 10576.399 3.1746032 377.27092 2.7176691 0.61999948 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 2 6 10304 3.0769231 443.36171 4.2093581 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 3 3 3680 4 32.805 0.10690769 0.9771554 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 3 4 14157.243 3.1914894 489.18197 2.5231391 0.45538909 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 3 5 6320.6076 3.6144578 103.50278 0.44181916 0.75109952 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 3 6 6157.8178 3.4883721 124.7792 0.72632262 0.73006542 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 4 4 54464 2.6548673 5679.4311 33.208515 0.34105936 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 4 5 24315.863 2.9411765 1371.5617 7.9168726 0.42457748 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 4 6 23689.598 2.8571429 1590.0769 11.87959 0.42066711 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 5 5 10856 3.2967033 308.7755 1.6022517 0.63272774 # buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 5 6 10576.399 3.1914894 365.45138 2.5231391 0.61999948 # buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 6 6 10304 3.0927835 429.89352 3.9170177 0.60800971 # buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
bond_style hybrid class2 morse
bond_coeff 5 morse 50.000000 1.451345 1.914000 # morse->(cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
bond_coeff 4 class2 2.536000 75.465060 -192.435903 286.248406 # mm3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2)|CuPW
bond_coeff 3 class2 1.094000 390.634200 -996.117210 1481.724350 # mm3->(c3_c2h1@ph,h1_c1@ph)|benzene
bond_coeff 6 class2 1.278000 585.591600 -1493.258580 2221.222138 # mm3->(c3_c1o2@co2,o2_c1cu1@co2)|CuPW
bond_coeff 1 class2 1.394000 509.335200 -1298.804760 1931.972080 # mm3->(c3_c2h1@ph,c3_c2h1@ph)|benzene
bond_coeff 2 class2 1.485000 360.635220 -919.619811 1367.934469 # mm3->(c3_c1o2@co2,c3_c3@ph)|CuPW
angle_style hybrid class2/p6 cosine/buck6d
angle_coeff 2 class2/p6 117.711000 57.408120 -46.049402 10.553745 -7.558563 13.610890 # mm3->(c3_c1o2@co2,c3_c3@ph,c3_c2h1@ph)|CuPW
angle_coeff 2 class2/p6 bb 0.0 1.0 1.0
angle_coeff 2 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 6 class2/p6 126.814000 13.740540 -11.021849 2.526022 -1.809130 3.257744 # mm3->(c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
angle_coeff 6 class2/p6 bb 0.0 1.0 1.0
angle_coeff 6 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 7 class2/p6 123.490000 111.075360 -89.098091 20.419778 -14.624589 26.334856 # mm3->(o2_c1cu1@co2,c3_c1o2@co2,o2_c1cu1@co2)|CuPW
angle_coeff 7 class2/p6 bb 14.244120 1.278000 1.278000
angle_coeff 7 class2/p6 ba 3.309240 3.309240 1.278000 1.278000
angle_coeff 1 class2/p6 127.050000 53.307540 -42.760159 9.799907 -7.018666 12.638684 # mm3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph)|benzene
angle_coeff 1 class2/p6 bb 71.796120 1.394000 1.394000
angle_coeff 1 class2/p6 ba 6.762360 6.762360 1.394000 1.394000
angle_coeff 4 class2/p6 84.336000 29.351520 -23.544055 5.395900 -3.864529 6.958951 # mm3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
angle_coeff 4 class2/p6 bb 0.0 1.0 1.0
angle_coeff 4 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 3 class2/p6 120.350000 36.185820 -29.026127 6.652298 -4.764358 8.579296 # mm3->(c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
angle_coeff 3 class2/p6 bb 93.378120 1.394000 1.094000
angle_coeff 3 class2/p6 ba -25.179000 53.523360 1.394000 1.094000
angle_coeff 8 class2/p6 115.098000 79.493700 -63.765149 14.613896 -10.466432 18.847160 # mm3->(c3_c3@ph,c3_c1o2@co2,o2_c1cu1@co2)|CuPW
angle_coeff 8 class2/p6 bb 0.0 1.0 1.0
angle_coeff 8 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 5 cosine/buck6d 1.978350 4 180.000000 # fourier->(o2_c1cu1@co2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
dihedral_style opls
dihedral_coeff 3 0.000000 0.000000 0.000000 0.000000 # cos3->(c3_c3@ph,c3_c2h1@ph,c3_c3@ph,c3_c1o2@co2)|CuPW
dihedral_coeff 9 0.000000 4.528000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
dihedral_coeff 8 0.000000 0.000000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,cu5_cu1o4@cu2,o2_c1cu1@co2,c3_c1o2@co2)|CuPW
dihedral_coeff 5 0.000000 1.741000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,c3_c1o2@co2,c3_c3@ph,c3_c2h1@ph)|CuPW
dihedral_coeff 2 0.000000 6.316000 0.000000 0.000000 # cos3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
dihedral_coeff 1 0.000000 4.379000 0.000000 0.000000 # cos3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph)|benzene
dihedral_coeff 6 0.000000 0.000000 0.000000 0.609000 # cos4->(o2_c1cu1@co2,cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
dihedral_coeff 4 0.000000 0.000000 0.000000 0.000000 # cos3->(h1_c1@ph,c3_c2h1@ph,c3_c3@ph,c3_c1o2@co2)|CuPW
dihedral_coeff 10 0.000000 0.000000 0.000000 0.000000 # cos3->(c3_c3@ph,c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
dihedral_coeff 7 0.000000 0.000000 0.000000 0.000000 # cos3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2,c3_c1o2@co2)|CuPW
improper_style inversion/harmonic
improper_coeff 1 18.776340 0.000000 # harm->(c3_c3@ph,c3_c2h1@ph,c3_c2h1@ph,c3_c1o2@co2)|CuPW
improper_coeff 3 41.005800 0.000000 # harm->(c3_c1o2@co2,c3_c3@ph,o2_c1cu1@co2,o2_c1cu1@co2)|CuPW
improper_coeff 2 4.100580 0.000000 # harm->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0
5 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of special neighbors
# ------------------------ MOF-FF FORCE FIELD END --------------------------
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair buck6d/coul/gauss/dsf, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 20.68 | 20.68 | 20.68 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -11833.81 343.7619 -11490.048 -5.8508834
Loop time of 2.20537e-06 on 4 procs for 0 steps with 624 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.205e-06 | | |100.00
Nlocal: 156 ave 156 max 156 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2718 ave 2718 max 2718 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 28842 ave 28870 max 28814 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 115368
Ave neighs/atom = 184.885
Ave special neighs/atom = 7.46154
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

175
examples/USER/mofff/log.17Jan18.hkust1_long.g++.1 Normal file
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LAMMPS (17 Jan 2018)
clear
units real
boundary p p p
atom_style full
read_data hkust1.data
triclinic box = (0 0 0) to (26.4408 26.4408 26.4408) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
624 atoms
scanning bonds ...
5 = max bonds/atom
scanning angles ...
10 = max angles/atom
scanning dihedrals ...
32 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
792 bonds
reading angles ...
1536 angles
reading dihedrals ...
2688 dihedrals
reading impropers ...
288 impropers
5 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
20 = max # of 1-4 neighbors
17 = max # of special neighbors
neighbor 2.0 bin
# ------------------------ MOF-FF FORCE FIELD ------------------------------
kspace_style ewald 1.0e-6
pair_style buck6d/coul/gauss/long 0.9 0.9 12.0000
pair_coeff 1 1 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW
pair_coeff 1 2 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene
pair_coeff 1 3 6157.8178 3.4682081 129.19572 0.78772886 0.73006542 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 1 4 23689.598 2.8436019 1636.052 12.696549 0.42066711 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 1 5 10576.399 3.1746032 377.27092 2.7176691 0.61999948 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 1 6 10304 3.0769231 443.36171 4.2093581 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 2 2 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene
pair_coeff 2 3 6157.8178 3.4682081 129.19572 0.78772886 0.73006542 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 2 4 23689.598 2.8436019 1636.052 12.696549 0.42066711 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 2 5 10576.399 3.1746032 377.27092 2.7176691 0.61999948 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 2 6 10304 3.0769231 443.36171 4.2093581 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 3 3 3680 4 32.805 0.10690769 0.9771554 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 3 4 14157.243 3.1914894 489.18197 2.5231391 0.45538909 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 3 5 6320.6076 3.6144578 103.50278 0.44181916 0.75109952 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 3 6 6157.8178 3.4883721 124.7792 0.72632262 0.73006542 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 4 4 54464 2.6548673 5679.4311 33.208515 0.34105936 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 4 5 24315.863 2.9411765 1371.5617 7.9168726 0.42457748 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 4 6 23689.598 2.8571429 1590.0769 11.87959 0.42066711 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 5 5 10856 3.2967033 308.7755 1.6022517 0.63272774 # buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 5 6 10576.399 3.1914894 365.45138 2.5231391 0.61999948 # buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 6 6 10304 3.0927835 429.89352 3.9170177 0.60800971 # buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
bond_style hybrid class2 morse
bond_coeff 5 morse 50.000000 1.451345 1.914000 # morse->(cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
bond_coeff 4 class2 2.536000 75.465060 -192.435903 286.248406 # mm3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2)|CuPW
bond_coeff 3 class2 1.094000 390.634200 -996.117210 1481.724350 # mm3->(c3_c2h1@ph,h1_c1@ph)|benzene
bond_coeff 6 class2 1.278000 585.591600 -1493.258580 2221.222138 # mm3->(c3_c1o2@co2,o2_c1cu1@co2)|CuPW
bond_coeff 1 class2 1.394000 509.335200 -1298.804760 1931.972080 # mm3->(c3_c2h1@ph,c3_c2h1@ph)|benzene
bond_coeff 2 class2 1.485000 360.635220 -919.619811 1367.934469 # mm3->(c3_c1o2@co2,c3_c3@ph)|CuPW
angle_style hybrid class2/p6 cosine/buck6d
angle_coeff 2 class2/p6 117.711000 57.408120 -46.049402 10.553745 -7.558563 13.610890 # mm3->(c3_c1o2@co2,c3_c3@ph,c3_c2h1@ph)|CuPW
angle_coeff 2 class2/p6 bb 0.0 1.0 1.0
angle_coeff 2 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 6 class2/p6 126.814000 13.740540 -11.021849 2.526022 -1.809130 3.257744 # mm3->(c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
angle_coeff 6 class2/p6 bb 0.0 1.0 1.0
angle_coeff 6 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 7 class2/p6 123.490000 111.075360 -89.098091 20.419778 -14.624589 26.334856 # mm3->(o2_c1cu1@co2,c3_c1o2@co2,o2_c1cu1@co2)|CuPW
angle_coeff 7 class2/p6 bb 14.244120 1.278000 1.278000
angle_coeff 7 class2/p6 ba 3.309240 3.309240 1.278000 1.278000
angle_coeff 1 class2/p6 127.050000 53.307540 -42.760159 9.799907 -7.018666 12.638684 # mm3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph)|benzene
angle_coeff 1 class2/p6 bb 71.796120 1.394000 1.394000
angle_coeff 1 class2/p6 ba 6.762360 6.762360 1.394000 1.394000
angle_coeff 4 class2/p6 84.336000 29.351520 -23.544055 5.395900 -3.864529 6.958951 # mm3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
angle_coeff 4 class2/p6 bb 0.0 1.0 1.0
angle_coeff 4 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 3 class2/p6 120.350000 36.185820 -29.026127 6.652298 -4.764358 8.579296 # mm3->(c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
angle_coeff 3 class2/p6 bb 93.378120 1.394000 1.094000
angle_coeff 3 class2/p6 ba -25.179000 53.523360 1.394000 1.094000
angle_coeff 8 class2/p6 115.098000 79.493700 -63.765149 14.613896 -10.466432 18.847160 # mm3->(c3_c3@ph,c3_c1o2@co2,o2_c1cu1@co2)|CuPW
angle_coeff 8 class2/p6 bb 0.0 1.0 1.0
angle_coeff 8 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 5 cosine/buck6d 1.978350 4 180.000000 #1.0 # fourier->(o2_c1cu1@co2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
dihedral_style opls
dihedral_coeff 3 0.000000 0.000000 0.000000 0.000000 # cos3->(c3_c3@ph,c3_c2h1@ph,c3_c3@ph,c3_c1o2@co2)|CuPW
dihedral_coeff 9 0.000000 4.528000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
dihedral_coeff 8 0.000000 0.000000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,cu5_cu1o4@cu2,o2_c1cu1@co2,c3_c1o2@co2)|CuPW
dihedral_coeff 5 0.000000 1.741000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,c3_c1o2@co2,c3_c3@ph,c3_c2h1@ph)|CuPW
dihedral_coeff 2 0.000000 6.316000 0.000000 0.000000 # cos3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
dihedral_coeff 1 0.000000 4.379000 0.000000 0.000000 # cos3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph)|benzene
dihedral_coeff 6 0.000000 0.000000 0.000000 0.609000 # cos4->(o2_c1cu1@co2,cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
dihedral_coeff 4 0.000000 0.000000 0.000000 0.000000 # cos3->(h1_c1@ph,c3_c2h1@ph,c3_c3@ph,c3_c1o2@co2)|CuPW
dihedral_coeff 10 0.000000 0.000000 0.000000 0.000000 # cos3->(c3_c3@ph,c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
dihedral_coeff 7 0.000000 0.000000 0.000000 0.000000 # cos3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2,c3_c1o2@co2)|CuPW
improper_style inversion/harmonic
improper_coeff 1 18.776340 0.000000 # harm->(c3_c3@ph,c3_c2h1@ph,c3_c2h1@ph,c3_c1o2@co2)|CuPW
improper_coeff 3 41.005800 0.000000 # harm->(c3_c1o2@co2,c3_c3@ph,o2_c1cu1@co2,o2_c1cu1@co2)|CuPW
improper_coeff 2 4.100580 0.000000 # harm->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0
5 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of special neighbors
# ------------------------ MOF-FF FORCE FIELD END --------------------------
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.267593
estimated absolute RMS force accuracy = 0.000333665
estimated relative force accuracy = 1.00482e-06
KSpace vectors: actual max1d max3d = 1054 8 2456
kxmax kymax kzmax = 8 8 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair buck6d/coul/gauss/long, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 34.64 | 34.64 | 34.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16541.109 343.7619 -16197.347 -629.64956
Loop time of 9.53674e-07 on 1 procs for 0 steps with 624 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 624 ave 624 max 624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4464 ave 4464 max 4464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 115368 ave 115368 max 115368 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 115368
Ave neighs/atom = 184.885
Ave special neighs/atom = 7.46154
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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examples/USER/mofff/log.17Jan18.hkust1_long.g++.4 Normal file
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LAMMPS (17 Jan 2018)
clear
units real
boundary p p p
atom_style full
read_data hkust1.data
triclinic box = (0 0 0) to (26.4408 26.4408 26.4408) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
624 atoms
scanning bonds ...
5 = max bonds/atom
scanning angles ...
10 = max angles/atom
scanning dihedrals ...
32 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
792 bonds
reading angles ...
1536 angles
reading dihedrals ...
2688 dihedrals
reading impropers ...
288 impropers
5 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
20 = max # of 1-4 neighbors
17 = max # of special neighbors
neighbor 2.0 bin
# ------------------------ MOF-FF FORCE FIELD ------------------------------
kspace_style ewald 1.0e-6
pair_style buck6d/coul/gauss/long 0.9 0.9 12.0000
pair_coeff 1 1 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW
pair_coeff 1 2 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene
pair_coeff 1 3 6157.8178 3.4682081 129.19572 0.78772886 0.73006542 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 1 4 23689.598 2.8436019 1636.052 12.696549 0.42066711 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 1 5 10576.399 3.1746032 377.27092 2.7176691 0.61999948 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 1 6 10304 3.0769231 443.36171 4.2093581 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c3@ph)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 2 2 10304 3.0612245 457.17971 4.5218516 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene
pair_coeff 2 3 6157.8178 3.4682081 129.19572 0.78772886 0.73006542 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 2 4 23689.598 2.8436019 1636.052 12.696549 0.42066711 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 2 5 10576.399 3.1746032 377.27092 2.7176691 0.61999948 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 2 6 10304 3.0769231 443.36171 4.2093581 0.60800971 # buck6d->(c3_c2h1@ph)|benzene/gaussian->(c3_c2h1@ph)|benzene <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 3 3 3680 4 32.805 0.10690769 0.9771554 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene
pair_coeff 3 4 14157.243 3.1914894 489.18197 2.5231391 0.45538909 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 3 5 6320.6076 3.6144578 103.50278 0.44181916 0.75109952 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 3 6 6157.8178 3.4883721 124.7792 0.72632262 0.73006542 # buck6d->(h1_c1@ph)|benzene/gaussian->(h1_c1@ph)|benzene <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 4 4 54464 2.6548673 5679.4311 33.208515 0.34105936 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW
pair_coeff 4 5 24315.863 2.9411765 1371.5617 7.9168726 0.42457748 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 4 6 23689.598 2.8571429 1590.0769 11.87959 0.42066711 # buck6d->(cu5_cu1o4@cu2)|CuPW/gaussian->(cu5_cu1o4@cu2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 5 5 10856 3.2967033 308.7755 1.6022517 0.63272774 # buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW <--> buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW
pair_coeff 5 6 10576.399 3.1914894 365.45138 2.5231391 0.61999948 # buck6d->(o2_c1cu1@co2)|CuPW/gaussian->(o2_c1cu1@co2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
pair_coeff 6 6 10304 3.0927835 429.89352 3.9170177 0.60800971 # buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW <--> buck6d->(c3_c1o2@co2)|CuPW/gaussian->(c3_c1o2@co2)|CuPW
bond_style hybrid class2 morse
bond_coeff 5 morse 50.000000 1.451345 1.914000 # morse->(cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
bond_coeff 4 class2 2.536000 75.465060 -192.435903 286.248406 # mm3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2)|CuPW
bond_coeff 3 class2 1.094000 390.634200 -996.117210 1481.724350 # mm3->(c3_c2h1@ph,h1_c1@ph)|benzene
bond_coeff 6 class2 1.278000 585.591600 -1493.258580 2221.222138 # mm3->(c3_c1o2@co2,o2_c1cu1@co2)|CuPW
bond_coeff 1 class2 1.394000 509.335200 -1298.804760 1931.972080 # mm3->(c3_c2h1@ph,c3_c2h1@ph)|benzene
bond_coeff 2 class2 1.485000 360.635220 -919.619811 1367.934469 # mm3->(c3_c1o2@co2,c3_c3@ph)|CuPW
angle_style hybrid class2/p6 cosine/buck6d
angle_coeff 2 class2/p6 117.711000 57.408120 -46.049402 10.553745 -7.558563 13.610890 # mm3->(c3_c1o2@co2,c3_c3@ph,c3_c2h1@ph)|CuPW
angle_coeff 2 class2/p6 bb 0.0 1.0 1.0
angle_coeff 2 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 6 class2/p6 126.814000 13.740540 -11.021849 2.526022 -1.809130 3.257744 # mm3->(c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
angle_coeff 6 class2/p6 bb 0.0 1.0 1.0
angle_coeff 6 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 7 class2/p6 123.490000 111.075360 -89.098091 20.419778 -14.624589 26.334856 # mm3->(o2_c1cu1@co2,c3_c1o2@co2,o2_c1cu1@co2)|CuPW
angle_coeff 7 class2/p6 bb 14.244120 1.278000 1.278000
angle_coeff 7 class2/p6 ba 3.309240 3.309240 1.278000 1.278000
angle_coeff 1 class2/p6 127.050000 53.307540 -42.760159 9.799907 -7.018666 12.638684 # mm3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph)|benzene
angle_coeff 1 class2/p6 bb 71.796120 1.394000 1.394000
angle_coeff 1 class2/p6 ba 6.762360 6.762360 1.394000 1.394000
angle_coeff 4 class2/p6 84.336000 29.351520 -23.544055 5.395900 -3.864529 6.958951 # mm3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
angle_coeff 4 class2/p6 bb 0.0 1.0 1.0
angle_coeff 4 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 3 class2/p6 120.350000 36.185820 -29.026127 6.652298 -4.764358 8.579296 # mm3->(c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
angle_coeff 3 class2/p6 bb 93.378120 1.394000 1.094000
angle_coeff 3 class2/p6 ba -25.179000 53.523360 1.394000 1.094000
angle_coeff 8 class2/p6 115.098000 79.493700 -63.765149 14.613896 -10.466432 18.847160 # mm3->(c3_c3@ph,c3_c1o2@co2,o2_c1cu1@co2)|CuPW
angle_coeff 8 class2/p6 bb 0.0 1.0 1.0
angle_coeff 8 class2/p6 ba 0.0 0.0 1.0 1.0
angle_coeff 5 cosine/buck6d 1.978350 4 180.000000 #1.0 # fourier->(o2_c1cu1@co2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
dihedral_style opls
dihedral_coeff 3 0.000000 0.000000 0.000000 0.000000 # cos3->(c3_c3@ph,c3_c2h1@ph,c3_c3@ph,c3_c1o2@co2)|CuPW
dihedral_coeff 9 0.000000 4.528000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
dihedral_coeff 8 0.000000 0.000000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,cu5_cu1o4@cu2,o2_c1cu1@co2,c3_c1o2@co2)|CuPW
dihedral_coeff 5 0.000000 1.741000 0.000000 0.000000 # cos3->(o2_c1cu1@co2,c3_c1o2@co2,c3_c3@ph,c3_c2h1@ph)|CuPW
dihedral_coeff 2 0.000000 6.316000 0.000000 0.000000 # cos3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
dihedral_coeff 1 0.000000 4.379000 0.000000 0.000000 # cos3->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph)|benzene
dihedral_coeff 6 0.000000 0.000000 0.000000 0.609000 # cos4->(o2_c1cu1@co2,cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2)|CuPW
dihedral_coeff 4 0.000000 0.000000 0.000000 0.000000 # cos3->(h1_c1@ph,c3_c2h1@ph,c3_c3@ph,c3_c1o2@co2)|CuPW
dihedral_coeff 10 0.000000 0.000000 0.000000 0.000000 # cos3->(c3_c3@ph,c3_c1o2@co2,o2_c1cu1@co2,cu5_cu1o4@cu2)|CuPW
dihedral_coeff 7 0.000000 0.000000 0.000000 0.000000 # cos3->(cu5_cu1o4@cu2,cu5_cu1o4@cu2,o2_c1cu1@co2,c3_c1o2@co2)|CuPW
improper_style inversion/harmonic
improper_coeff 1 18.776340 0.000000 # harm->(c3_c3@ph,c3_c2h1@ph,c3_c2h1@ph,c3_c1o2@co2)|CuPW
improper_coeff 3 41.005800 0.000000 # harm->(c3_c1o2@co2,c3_c3@ph,o2_c1cu1@co2,o2_c1cu1@co2)|CuPW
improper_coeff 2 4.100580 0.000000 # harm->(c3_c2h1@ph,c3_c2h1@ph,c3_c2h1@ph,h1_c1@ph)|benzene
special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0
5 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of special neighbors
# ------------------------ MOF-FF FORCE FIELD END --------------------------
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.267593
estimated absolute RMS force accuracy = 0.000333665
estimated relative force accuracy = 1.00482e-06
KSpace vectors: actual max1d max3d = 1054 8 2456
kxmax kymax kzmax = 8 8 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair buck6d/coul/gauss/long, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 34.1 | 34.1 | 34.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16541.109 343.7619 -16197.347 -629.64956
Loop time of 6.13928e-06 on 4 procs for 0 steps with 624 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 6.139e-06 | | |100.00
Nlocal: 156 ave 156 max 156 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2718 ave 2718 max 2718 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 28842 ave 28870 max 28814 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 115368
Ave neighs/atom = 184.885
Ave special neighs/atom = 7.46154
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00