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log.lammps
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LAMMPS (22 Aug 2018)
variable rseed equal 4928459
# ---- Settings ----
variable hT equal 3.0
variable T equal 1.0
units lj
atom_style full
bond_style class2
boundary s s s
special_bonds lj 0.0 0.0 1.0 extra 512
read_data ../../../../inputFiles/lmps_input/Gm12878/data.chromosome.chr1
orthogonal box = (-12.869 -13.783 -12.466) to (12.928 13.119 12.86)
1 by 1 by 1 MPI processor grid
reading atoms ...
5000 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4999 bonds
reading angles ...
4998 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
518 = max # of special neighbors
neighbor 0.4 bin
neigh_modify every 1 delay 1
atom_modify sort 0 0.0
# ---- Force Field ----
bond_coeff 1 2.0 20.0 20.0 20.0
angle_style cosine
angle_coeff 1 2.0
# ---- Energy funtion ----
pair_style hybrid/overlay table linear 10000 tanhlr/cut/ideala 6.0 0 15 /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/../src/md/lmps_input//ucs_chrom.txt /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/inputFiles/epig_input/chromStates/Gm12878/Gm12878_chr1_chromatin_states_From20MbTo45Mb.txt tanhlr/cut/ideal 6.0 /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/../src/md/lmps_input//uctcf_chrom.txt /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/inputFiles/epig_input/ctcfSites/Gm12878/Gm12878_chr1_ctcf_index_From20MbTo45Mb.txt 4
pair_coeff * * table /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/../src/md/lmps_input//soft_core_lj_4kT.table soft_core_lj 1.12
WARNING: 4174 of 10006 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
WARNING: 9976 of 10006 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:490)
WARNING: 1 of 10006 lines in table were incomplete
or could not be parsed completely (../pair_table.cpp:499)
pair_coeff * * tanhlr/cut/ideal 0.0 1.76 3.72
pair_coeff * * tanhlr/cut/ideala 0.0 1.76 3.72
pair_modify tabinner 0.0000000001 shift yes
thermo 10000
thermo_style custom time temp pe etotal epair ebond eangle press vol
thermo_modify norm no flush yes
# ---- Spherical confinement ----
region nucleus sphere 0.0 0.0 0.0 26.56193 side in
fix wall all wall/region nucleus lj126 1.0 1.0 1.12
# ---- Minimization ----
minimize 1.0e-4 1.0e-6 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.4
ghost atom cutoff = 6.4
binsize = 3.2, bins = 9 9 8
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair tanhlr/cut/ideala, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) pair tanhlr/cut/ideal, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 28.28 | 28.28 | 28.28 Mbytes
Time Temp PotEng TotEng E_pair E_bond E_angle Press Volume
0 0 122720.58 122720.58 -9440.7181 124796.82 7364.4717 5.6285236 17506.974
0.5 0 1971.6667 1971.6667 -9815.8443 133.27032 11654.241 -0.18202516 20245.42
Loop time of 12.71 on 1 procs for 100 steps with 5000 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
122720.577169 2014.92815556 1971.66674767
Force two-norm initial, final = 6753.72 70.9161
Force max component initial, final = 279.983 14.5162
Final line search alpha, max atom move = 0.00580849 0.0843173
Iterations, force evaluations = 100 100
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.551 | 11.551 | 11.551 | 0.0 | 90.88
Bond | 0.051005 | 0.051005 | 0.051005 | 0.0 | 0.40
Neigh | 1.0718 | 1.0718 | 1.0718 | 0.0 | 8.43
Comm | 0.001524 | 0.001524 | 0.001524 | 0.0 | 0.01
Output | 0.00017309 | 0.00017309 | 0.00017309 | 0.0 | 0.00
Modify | 0.013068 | 0.013068 | 0.013068 | 0.0 | 0.10
Other | | 0.02132 | | | 0.17
Nlocal: 5000 ave 5000 max 5000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.26854e+06 ave 1.26854e+06 max 1.26854e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1268544
Ave neighs/atom = 253.709
Ave special neighs/atom = 5.9976
Neighbor list builds = 26
Dangerous builds = 0
# ---- Energy and velocity ----
fix 1 all nve
velocity all create ${hT} ${rseed} rot yes mom yes dist gaussian
velocity all create 3 ${rseed} rot yes mom yes dist gaussian
velocity all create 3 4928459 rot yes mom yes dist gaussian
# ---- High temperature equilibration ----
#dump 1 all dcd 2000 DUMP_FILE_highT.dcd
#dump_modify 1 unwrap yes
#timestep 0.006
#fix 2 all langevin ${hT} ${T} 0.5 ${rseed}
#run 4000000
# ---- Normal temperature ----
#undump 1
#unfix 2
dump 2 all dcd 2000 DUMP_FILE.dcd
dump_modify 2 unwrap yes
timestep 0.012
fix 3 all langevin ${T} ${T} 0.5 ${rseed}
fix 3 all langevin 1 ${T} 0.5 ${rseed}
fix 3 all langevin 1 1 0.5 ${rseed}
fix 3 all langevin 1 1 0.5 4928459
run 40000000
Per MPI rank memory allocation (min/avg/max) = 27.99 | 27.99 | 27.99 Mbytes
Time Temp PotEng TotEng E_pair E_bond E_angle Press Volume
0 3 1971.6667 24467.167 -9815.8443 133.27032 11654.241 0.55955945 20215.59