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Merge pull request #1180 from gtribello/master

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Add natively supported PLUMED interface to LAMMPS
This commit is contained in:
Axel Kohlmeyer
2018-11-08 16:16:50 -05:00
committed by GitHub
parent 893a51ce14 ce7f76de1d
commit a6e9b99295
23 changed files with 8333 additions and 6 deletions
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# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
group one id 2 4 5 6
group two id 80 82 83 84
group ref id 37
group colvar union one two ref
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all plumed plumedfile plumed.dat outfile p.log
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
variable step equal step
variable pe equal pe
run 101

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LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all plumed plumedfile plumed.dat outfile p.log
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
variable step equal step
variable pe equal pe
run 101
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
20 279.08532 -5226.4036 -6349.1917 1122.7881 -6441.0169 20.764378 0.52605302
30 282.32141 -5222.3866 -6358.1939 1135.8073 -6448.9785 22.945165 0.65106011
40 276.34173 -5218.7623 -6330.5128 1111.7504 -6423.7566 15.655345 0.23795099
50 286.12741 -5215.9248 -6367.0439 1151.1192 -6449.2655 17.420975 0.42646205
60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815
70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896
80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348
90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014
SHAKE stats (type/ave/delta) on step 100
4 1.111 2.06868e-06
6 0.996999 2.09521e-06
8 1.08 1.10835e-06
10 1.111 2.46599e-06
12 1.08 8.86314e-07
14 0.959999 0
18 0.9572 9.14098e-06
31 104.52 0.000760401
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
Loop time of 2.12948 on 1 procs for 101 steps with 2004 atoms
Performance: 8.196 ns/day, 2.928 hours/ns, 47.429 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.757 | 1.757 | 1.757 | 0.0 | 82.51
Bond | 0.0052233 | 0.0052233 | 0.0052233 | 0.0 | 0.25
Kspace | 0.14772 | 0.14772 | 0.14772 | 0.0 | 6.94
Neigh | 0.16455 | 0.16455 | 0.16455 | 0.0 | 7.73
Comm | 0.0083704 | 0.0083704 | 0.0083704 | 0.0 | 0.39
Output | 0.00031424 | 0.00031424 | 0.00031424 | 0.0 | 0.01
Modify | 0.044411 | 0.044411 | 0.044411 | 0.0 | 2.09
Other | | 0.001851 | | | 0.09
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11134 ave 11134 max 11134 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 707961 ave 707961 max 707961 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 707961
Ave neighs/atom = 353.274
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all plumed plumedfile plumed.dat outfile p.log
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
variable step equal step
variable pe equal pe
run 101
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
20 279.08532 -5226.4036 -6349.1917 1122.7881 -6441.0169 20.764378 0.52605302
30 282.32141 -5222.3866 -6358.1939 1135.8073 -6448.9785 22.945165 0.65106011
40 276.34173 -5218.7623 -6330.5128 1111.7504 -6423.7566 15.655345 0.23795099
50 286.12741 -5215.9248 -6367.0439 1151.1192 -6449.2655 17.420975 0.42646205
60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815
70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896
80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348
90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3466 21.124789 0.5468014
SHAKE stats (type/ave/delta) on step 100
4 1.111 2.06868e-06
6 0.996999 2.09521e-06
8 1.08 1.10835e-06
10 1.111 2.46599e-06
12 1.08 8.86314e-07
14 0.959999 0
18 0.9572 9.14098e-06
31 104.52 0.000760401
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.009478437
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
Loop time of 1.16767 on 4 procs for 101 steps with 2004 atoms
Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.84633 | 0.86651 | 0.88617 | 1.6 | 74.21
Bond | 0.0010614 | 0.0027132 | 0.004288 | 3.0 | 0.23
Kspace | 0.095008 | 0.1162 | 0.13491 | 4.3 | 9.95
Neigh | 0.07834 | 0.078424 | 0.078516 | 0.0 | 6.72
Comm | 0.03314 | 0.033299 | 0.033426 | 0.1 | 2.85
Output | 0.00036979 | 0.00076199 | 0.0019338 | 0.0 | 0.07
Modify | 0.063471 | 0.064011 | 0.065312 | 0.3 | 5.48
Other | | 0.005751 | | | 0.49
Nlocal: 501 ave 512 max 492 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 6570.25 ave 6604 max 6529 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 176990 ave 181122 max 173551 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 707961
Ave neighs/atom = 353.274
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:01

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UNITS LENGTH=A ENERGY=kcal/mol
dd: DISTANCE ATOMS=45,48
RESTRAINT ARG=dd KAPPA=2000 AT=6.0
PRINT ARG=dd FILE=colvar

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#! FIELDS time dd
0.000000 5.985554
0.002000 6.002880
0.004000 6.022015
0.006000 6.029922
0.008000 6.020103
0.010000 5.996906
0.012000 5.972734
0.014000 5.960079
0.016000 5.963714
0.018000 5.978140
0.020000 5.991813
0.022000 5.995155
0.024000 5.987021
0.026000 5.975340
0.028000 5.971456
0.030000 5.981945
0.032000 6.003550
0.034000 6.024743
0.036000 6.032990
0.038000 6.022936
0.040000 6.000131
0.042000 5.977800
0.044000 5.968692
0.046000 5.977224
0.048000 5.996934
0.050000 6.014800
0.052000 6.019586
0.054000 6.008803
0.056000 5.989809
0.058000 5.974484
0.060000 5.971140
0.062000 5.979074
0.064000 5.989379
0.066000 5.991356
0.068000 5.980176
0.070000 5.960625
0.072000 5.944401
0.074000 5.942614
0.076000 5.958402
0.078000 5.984574
0.080000 6.007964
0.082000 6.017667
0.084000 6.011795
0.086000 5.998304
0.088000 5.989405
0.090000 5.993275
0.092000 6.008545
0.094000 6.025183
0.096000 6.031186
0.098000 6.020651
0.100000 5.997952
0.102000 5.975230
0.104000 5.964757
0.106000 5.971150
0.108000 5.988568
0.110000 6.004676
0.112000 6.008731
0.114000 5.998481
0.116000 5.981406
0.118000 5.969615
0.120000 5.971827
0.122000 5.987658
0.124000 6.007888
0.126000 6.020477
0.128000 6.018377
0.130000 6.004046
0.132000 5.987682
0.134000 5.980338
0.136000 5.986534
0.138000 6.001303
0.140000 6.013589
0.142000 6.013717
0.144000 6.000028
0.146000 5.980283
0.148000 5.966836
0.150000 5.968670
0.152000 5.985459
0.154000 6.007612
0.156000 6.022374
0.158000 6.022034
0.160000 6.008851
0.162000 5.993355
0.164000 5.987212
0.166000 5.995452
0.168000 6.013111
0.170000 6.028386
0.172000 6.030387
0.174000 6.016468
0.176000 5.994191
0.178000 5.976616
0.180000 5.973983
0.182000 5.987185
0.184000 6.007275
0.186000 6.021338
0.188000 6.020837
0.190000 6.006955
0.192000 5.989433
0.194000 5.979796
0.196000 5.983601
0.198000 5.996921
0.200000 6.009310
0.202000 6.011114

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PLUMED: PLUMED is starting
PLUMED: Version: 2.4.2 (git: Unknown) compiled on Jul 11 2018 at 19:09:03
PLUMED: Please cite this paper when using PLUMED [1]
PLUMED: For further information see the PLUMED web page at http://www.plumed.org
PLUMED: Root: /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2/
PLUMED: For installed feature, see /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2//src/config/config.txt
PLUMED: Molecular dynamics engine: LAMMPS
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 2004
PLUMED: File suffix:
PLUMED: FILE: plumed.dat
PLUMED: Action UNITS
PLUMED: with label @0
PLUMED: length: A
PLUMED: energy: kcal/mol
PLUMED: time: ps
PLUMED: charge: e
PLUMED: mass: amu
PLUMED: using physical units
PLUMED: inside PLUMED, Boltzmann constant is 0.001987
PLUMED: Action DISTANCE
PLUMED: with label dd
PLUMED: between atoms 45 48
PLUMED: using periodic boundary conditions
PLUMED: Action RESTRAINT
PLUMED: with label @2
PLUMED: with arguments dd
PLUMED: added component to this action: @2.bias
PLUMED: at 6.000000
PLUMED: with harmonic force constant 2000.000000
PLUMED: and linear force constant 0.000000
PLUMED: added component to this action: @2.force2
PLUMED: Action PRINT
PLUMED: with label @3
PLUMED: with stride 1
PLUMED: with arguments dd
PLUMED: on file colvar
PLUMED: with format %f
PLUMED: END FILE: plumed.dat
PLUMED: Timestep: 0.002000
PLUMED: KbT has not been set by the MD engine
PLUMED: It should be set by hand where needed
PLUMED: Relevant bibliography:
PLUMED: [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
PLUMED: Cycles Total Average Minumum Maximum
PLUMED: 1 0.020354 0.020354 0.020354 0.020354
PLUMED: 1 Prepare dependencies 102 0.000256 0.000003 0.000001 0.000006
PLUMED: 2 Sharing data 102 0.010002 0.000098 0.000078 0.000546
PLUMED: 3 Waiting for data 102 0.001398 0.000014 0.000011 0.000072
PLUMED: 4 Calculating (forward loop) 102 0.001797 0.000018 0.000013 0.000058
PLUMED: 5 Applying (backward loop) 102 0.002666 0.000026 0.000022 0.000062
PLUMED: 6 Update 102 0.001126 0.000011 0.000007 0.000055